[maker-devel] MAKER Commercial User -- Install and run issues
Hayley Mangelson
hayley at phasegenomics.com
Fri Aug 11 07:20:14 MDT 2023
Hi Carson,
Sure thing! Sorry for the delay, I was on vacation. I reran with just a
single scaffold. Here is the STDERR.
On Mon, Jul 31, 2023 at 12:06 PM Carson Holt <carsonhh at gmail.com> wrote:
> Can you send me the STDERR from the maker run? If you don’t have it, run
> maker again with the output from the screen redirected to a file. Example
> —> maker &> all_output.txt
>
> --Carson
>
> Sent from my iPhone
>
> On Jul 31, 2023, at 10:04 AM, Hayley Mangelson <hayley at phasegenomics.com>
> wrote:
>
>
> Hi!
>
> I am trying to get a fresh install of MAKER to work for me and am having a
> few issues.
>
> 1. I got MAKER installed (I thought) and now the log is saying all contigs
> failed. See attached log.
> 2. Having tried several versions and methods of installation, I cannot get
> multithreading to work.
>
> Could you help me work through these issues?
> Thanks,
>
> Hayley
> --
> Hayley Mangelson
> Senior Bioinformatics Lead
> Phase Genomics, Inc
> www.phasegenomics.com
>
> <PGA_assembly_hap1_master_datastore_index.log>
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>
>
--
Hayley Mangelson
Senior Bioinformatics Lead
Phase Genomics, Inc
www.phasegenomics.com
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STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
A data structure will be created for you at:
/home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore
To access files for individual sequences use the datastore index:
/home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_master_datastore_index.log
STATUS: Now running MAKER...
examining contents of the fasta file and run log
--Next Contig--
#---------------------------------------------------------------------
Now starting the contig!!
SeqID: PGA_scaffold34__164_contigs__length_87950420
Length: 87950420
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.0.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.0.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype prot -in /tmp/maker_nNIkWB/0/blastprep/te_proteins%2Efasta.mpi.10.0
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype prot -in /tmp/maker_nNIkWB/0/blastprep/te_proteins%2Efasta.mpi.10.1
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype prot -in /tmp/maker_nNIkWB/0/blastprep/te_proteins%2Efasta.mpi.10.2
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype prot -in /tmp/maker_nNIkWB/0/blastprep/te_proteins%2Efasta.mpi.10.3
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype prot -in /tmp/maker_nNIkWB/0/blastprep/te_proteins%2Efasta.mpi.10.4
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype prot -in /tmp/maker_nNIkWB/0/blastprep/te_proteins%2Efasta.mpi.10.5
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype prot -in /tmp/maker_nNIkWB/0/blastprep/te_proteins%2Efasta.mpi.10.6
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype prot -in /tmp/maker_nNIkWB/0/blastprep/te_proteins%2Efasta.mpi.10.7
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype prot -in /tmp/maker_nNIkWB/0/blastprep/te_proteins%2Efasta.mpi.10.8
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/local/bin/makeblastdb -dbtype prot -in /tmp/maker_nNIkWB/0/blastprep/te_proteins%2Efasta.mpi.10.9
#-------------------------------#
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:4 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.1.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.1.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.1 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.1.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.2.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.2.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.2 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.2.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.3.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.3.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.3 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.3.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.4.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.4.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.4 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.4.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.5.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.5.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.5 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.5.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:2 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.6.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.6.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.6 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.6.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.7.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.7.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.7 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.7.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.8.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.8.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.8 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.8.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.9.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.9.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.9 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/0/PGA_scaffold34__164_contigs__length_87950420.9.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.10.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.10.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.10 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.10.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.11.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.11.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.11 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.11.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.12.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.12.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.12 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.12.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.13.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.13.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.13 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.13.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.14.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.14.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.14 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.14.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.15.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.15.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.15 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.15.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:2 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.16.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.16.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.16 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.16.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.17.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.17.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.17 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.17.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.18.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.18.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.18 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.18.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.19.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.19.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.19 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/1/PGA_scaffold34__164_contigs__length_87950420.19.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.20.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.20.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.20 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.20.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.21.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.21.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.21 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.21.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.22.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.22.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.22 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.22.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.23.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.23.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.23 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.23.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.24.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.24.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.24 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.24.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.25.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.25.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.25 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.25.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.26.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.26.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.26 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.26.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.27.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.27.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.27 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.27.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.28.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.28.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.28 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.28.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.29.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.29.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.29 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/2/PGA_scaffold34__164_contigs__length_87950420.29.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.30.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.30.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.30 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.30.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.31.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.31.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.31 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.31.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.32.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.32.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.32 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.32.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.33.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.33.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.33 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.33.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.34.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.34.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.34 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.34.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.35.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.35.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.35 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.35.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.36.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.36.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.36 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.36.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.37.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.37.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.37 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.37.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.38.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.38.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.38 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.38.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.39.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.39.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.39 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/3/PGA_scaffold34__164_contigs__length_87950420.39.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.40.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.40.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.40 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.40.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.41.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.41.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.41 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.41.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.42.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.42.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.42 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.42.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.43.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.43.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.43 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.43.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.44.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.44.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.44 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.44.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.45.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.45.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.45 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.45.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.46.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.46.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.46 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.46.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.47.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.47.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.47 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.47.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.48.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.48.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.48 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.48.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.49.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.49.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.49 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.49.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.49 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.49.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.49 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.49.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.49 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.49.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.49 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.49.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.49 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.49.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.49 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.49.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.49 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.49.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.49 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.49.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.49 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/4/PGA_scaffold34__164_contigs__length_87950420.49.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.50.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.50.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.50 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.50.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.50 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.50.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.50 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.50.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.50 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.50.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.50 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.50.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.50 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.50.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.50 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.50.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.50 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.50.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.50 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.50.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.50 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.50.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.51.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.51.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.51 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.51.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.51 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.51.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.51 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.51.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.51 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.51.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.51 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.51.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.51 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.51.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.51 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.51.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.51 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.51.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.51 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.51.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.51 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.51.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.52.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.52.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.52 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.52.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.52 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.52.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.52 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.52.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.52 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.52.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.52 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.52.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.52 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.52.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.52 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.52.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.52 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.52.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.52 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.52.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.52 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.52.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.53.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.53.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.53 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.53.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.53 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.53.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.53 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.53.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.53 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.53.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.53 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.53.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.53 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.53.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.53 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.53.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.53 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.53.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.53 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.53.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.53 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.53.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.54.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.54.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.54 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.54.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.54 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.54.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.54 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.54.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.54 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.54.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.54 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.54.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.54 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.54.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.54 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.54.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.54 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.54.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.54 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.54.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.54 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.54.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.55.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.55.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.55 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.55.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.55 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.55.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.55 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.55.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.55 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.55.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.55 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.55.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.55 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.55.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.55 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.55.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.55 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.55.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.55 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.55.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.55 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.55.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.56.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.56.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.56 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.56.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.56 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.56.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.56 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.56.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.56 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.56.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.56 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.56.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.56 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.56.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.56 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.56.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.56 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.56.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.56 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.56.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.56 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.56.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.57.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.57.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.57 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.57.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.57 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.57.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.57 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.57.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.57 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.57.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.57 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.57.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.57 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.57.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.57 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.57.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.57 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.57.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.57 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.57.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.57 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.57.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.58.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.58.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.58 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.58.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.58 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.58.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.58 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.58.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.58 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.58.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.58 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.58.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.58 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.58.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.58 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.58.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.58 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.58.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.58 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.58.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.58 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.58.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.59.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.59.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.59 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.59.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.59 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.59.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.59 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.59.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.59 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.59.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.59 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.59.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.59 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.59.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.59 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.59.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.59 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.59.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.59 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.59.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.59 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/5/PGA_scaffold34__164_contigs__length_87950420.59.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.60.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.60.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.60 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.60.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.60 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.60.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.60 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.60.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.60 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.60.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.60 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.60.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.60 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.60.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.60 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.60.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.60 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.60.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.60 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.60.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.60 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.60.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.61.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.61.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.61 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.61.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.61 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.61.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.61 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.61.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.61 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.61.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.61 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.61.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.61 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.61.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.61 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.61.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.61 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.61.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.61 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.61.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.61 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.61.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:2 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.62.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.62.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.62 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.62.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.62 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.62.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.62 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.62.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.62 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.62.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.62 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.62.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.62 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.62.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.62 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.62.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.62 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.62.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.62 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.62.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.62 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.62.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.63.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.63.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.63 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.63.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.63 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.63.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.63 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.63.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.63 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.63.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.63 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.63.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.63 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.63.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.63 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.63.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.63 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.63.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.63 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.63.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.63 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.63.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.64.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.64.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.64 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.64.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.64 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.64.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.64 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.64.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.64 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.64.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.64 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.64.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.64 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.64.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.64 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.64.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.64 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.64.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.64 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.64.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.64 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.64.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.65.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.65.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.65 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.65.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.65 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.65.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.65 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.65.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.65 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.65.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.65 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.65.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.65 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.65.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.65 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.65.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.65 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.65.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.65 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.65.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.65 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.65.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.66.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.66.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.66 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.66.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.66 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.66.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.66 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.66.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.66 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.66.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.66 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.66.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.66 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.66.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.66 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.66.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.66 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.66.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.66 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.66.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.66 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.66.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.67.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.67.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.67 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.67.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.67 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.67.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.67 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.67.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.67 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.67.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.67 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.67.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.67 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.67.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.67 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.67.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.67 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.67.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.67 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.67.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.67 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.67.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.68.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.68.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.68 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.68.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.68 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.68.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.68 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.68.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.68 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.68.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.68 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.68.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.68 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.68.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.68 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.68.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.68 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.68.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.68 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.68.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.68 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.68.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.69.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.69.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.69 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.69.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.69 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.69.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.69 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.69.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.69 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.69.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.69 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.69.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.69 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.69.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.69 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.69.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.69 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.69.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.69 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.69.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.69 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/6/PGA_scaffold34__164_contigs__length_87950420.69.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.70.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.70.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.70 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.70.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.70 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.70.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.70 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.70.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.70 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.70.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.70 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.70.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.70 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.70.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.70 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.70.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.70 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.70.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.70 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.70.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.70 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.70.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.71.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.71.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.71 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.71.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.71 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.71.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.71 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.71.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.71 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.71.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.71 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.71.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.71 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.71.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.71 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.71.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.71 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.71.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.71 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.71.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.71 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.71.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.72.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.72.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.72 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.72.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.72 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.72.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.72 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.72.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.72 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.72.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.72 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.72.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.72 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.72.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.72 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.72.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.72 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.72.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.72 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.72.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.72 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.72.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.73.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.73.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.73 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.73.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.73 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.73.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.73 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.73.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.73 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.73.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.73 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.73.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.73 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.73.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.73 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.73.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.73 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.73.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.73 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.73.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.73 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.73.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.74.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.74.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.74 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.74.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.74 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.74.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.74 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.74.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.74 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.74.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.74 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.74.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.74 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.74.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.74 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.74.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.74 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.74.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.74 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.74.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.74 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.74.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.75.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.75.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.75 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.75.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.75 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.75.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.75 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.75.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.75 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.75.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.75 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.75.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.75 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.75.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.75 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.75.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.75 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.75.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.75 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.75.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.75 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.75.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.76.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.76.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.76 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.76.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.76 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.76.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.76 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.76.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.76 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.76.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.76 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.76.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.76 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.76.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.76 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.76.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.76 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.76.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.76 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.76.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.76 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.76.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.77.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.77.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.77 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.77.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.77 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.77.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.77 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.77.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.77 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.77.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.77 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.77.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.77 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.77.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.77 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.77.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.77 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.77.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.77 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.77.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.77 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.77.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:2 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.78.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.78.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.78 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.78.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.78 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.78.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.78 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.78.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.78 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.78.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.78 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.78.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.78 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.78.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.78 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.78.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.78 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.78.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.78 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.78.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.78 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.78.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.79.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.79.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.79 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.79.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.79 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.79.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.79 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.79.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.79 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.79.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.79 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.79.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.79 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.79.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.79 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.79.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.79 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.79.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.79 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.79.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.79 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/7/PGA_scaffold34__164_contigs__length_87950420.79.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.80.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.80.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.80 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.80.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.80 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.80.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.80 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.80.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.80 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.80.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.80 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.80.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.80 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.80.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.80 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.80.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.80 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.80.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.80 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.80.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.80 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.80.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.81.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.81.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.81 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.81.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.81 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.81.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.81 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.81.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.81 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.81.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.81 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.81.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.81 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.81.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.81 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.81.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.81 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.81.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.81 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.81.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.81 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.81.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.82.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.82.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.82 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.82.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.82 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.82.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.82 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.82.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.82 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.82.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.82 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.82.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.82 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.82.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.82 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.82.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.82 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.82.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.82 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.82.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.82 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.82.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.83.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.83.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.83 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.83.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.83 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.83.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.83 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.83.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.83 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.83.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.83 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.83.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.83 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.83.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.83 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.83.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.83 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.83.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.83 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.83.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.83 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.83.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.84.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.84.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.84 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.84.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.84 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.84.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.84 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.84.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.84 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.84.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.84 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.84.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.84 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.84.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.84 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.84.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.84 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.84.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.84 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.84.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.84 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.84.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.85.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.85.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.85 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.85.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.85 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.85.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.85 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.85.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.85 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.85.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.85 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.85.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.85 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.85.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.85 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.85.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.85 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.85.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.85 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.85.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.85 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.85.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.86.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.86.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.86 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.86.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.86 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.86.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.86 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.86.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.86 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.86.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.86 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.86.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.86 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.86.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.86 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.86.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.86 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.86.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.86 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.86.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.86 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.86.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.87.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.87.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.87 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.87.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.87 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.87.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.87 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.87.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.87 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.87.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.87 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.87.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.87 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.87.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.87 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.87.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.87 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.87.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.87 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.87.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.87 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.87.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.88.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.88.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.88 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.88.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.88 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.88.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.88 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.88.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.88 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.88.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.88 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.88.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.88 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.88.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.88 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.88.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.88 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.88.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.88 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.88.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.88 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.88.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.89.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.89.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.89 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.89.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.89 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.89.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.89 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.89.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.89 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.89.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.89 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.89.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.89 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.89.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.89 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.89.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.89 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.89.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.89 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.89.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.89 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/8/PGA_scaffold34__164_contigs__length_87950420.89.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.90.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.90.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.90 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.90.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.90 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.90.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.90 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.90.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.90 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.90.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.90 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.90.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.90 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.90.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.90 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.90.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.90 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.90.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.90 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.90.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.90 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.90.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.91.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.91.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.91 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.91.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.91 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.91.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.91 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.91.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.91 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.91.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.91 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.91.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.91 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.91.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.91 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.91.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.91 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.91.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.91 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.91.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.91 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.91.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.92.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.92.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.92 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.92.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.92 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.92.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.92 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.92.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.92 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.92.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.92 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.92.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.92 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.92.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.92 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.92.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.92 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.92.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.92 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.92.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.92 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.92.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.93.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.93.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.93 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.93.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.93 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.93.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.93 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.93.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.93 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.93.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.93 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.93.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.93 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.93.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.93 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.93.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.93 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.93.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.93 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.93.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.93 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.93.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.94.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.94.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.94 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.94.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.94 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.94.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.94 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.94.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.94 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.94.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.94 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.94.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.94 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.94.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.94 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.94.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.94 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.94.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.94 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.94.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.94 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.94.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:2 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.95.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.95.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.95 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.95.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.95 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.95.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.95 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.95.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.95 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.95.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.95 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.95.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.95 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.95.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.95 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.95.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.95 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.95.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.95 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.95.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.95 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.95.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.96.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.96.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.96 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.96.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.96 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.96.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.96 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.96.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.96 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.96.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.96 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.96.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.96 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.96.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.96 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.96.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.96 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.96.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.96 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.96.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.96 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.96.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.97.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.97.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.97 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.97.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.97 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.97.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.97 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.97.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.97 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.97.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.97 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.97.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.97 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.97.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.97 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.97.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.97 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.97.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.97 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.97.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.97 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.97.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.98.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.98.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.98 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.98.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.98 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.98.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.98 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.98.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.98 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.98.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.98 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.98.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.98 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.98.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.98 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.98.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.98 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.98.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.98 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.98.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.98 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.98.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.99.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.99.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.99 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.99.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.99 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.99.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.99 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.99.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.99 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.99.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.99 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.99.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.99 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.99.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.99 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.99.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.99 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.99.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.99 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.99.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.99 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/9/PGA_scaffold34__164_contigs__length_87950420.99.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.100.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.100.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.100 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.100.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.100 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.100.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.100 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.100.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.100 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.100.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.100 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.100.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.100 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.100.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.100 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.100.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.100 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.100.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.100 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.100.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.100 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.100.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.101.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.101.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.101 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.101.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.101 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.101.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.101 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.101.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.101 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.101.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.101 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.101.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.101 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.101.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.101 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.101.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.101 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.101.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.101 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.101.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.101 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.101.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.102.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.102.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.102 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.102.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.102 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.102.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.102 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.102.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.102 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.102.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.102 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.102.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.102 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.102.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.102 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.102.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.102 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.102.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.102 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.102.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.102 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.102.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.103.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.103.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.103 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.103.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.103 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.103.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.103 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.103.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.103 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.103.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.103 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.103.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.103 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.103.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.103 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.103.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.103 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.103.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.103 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.103.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.103 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.103.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.104.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.104.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.104 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.104.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.104 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.104.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.104 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.104.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.104 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.104.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.104 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.104.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.104 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.104.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.104 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.104.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.104 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.104.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.104 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.104.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.104 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.104.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.105.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.105.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.105 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.105.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.105 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.105.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.105 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.105.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.105 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.105.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.105 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.105.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.105 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.105.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.105 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.105.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.105 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.105.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.105 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.105.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.105 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.105.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.106.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.106.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.106 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.106.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.106 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.106.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.106 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.106.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.106 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.106.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.106 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.106.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.106 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.106.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.106 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.106.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.106 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.106.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.106 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.106.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.106 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.106.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.107.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.107.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.107 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.107.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.107 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.107.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.107 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.107.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.107 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.107.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.107 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.107.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.107 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.107.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.107 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.107.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.107 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.107.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.107 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.107.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.107 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.107.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.108.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.108.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.108 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.108.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.108 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.108.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.108 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.108.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.108 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.108.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.108 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.108.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.108 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.108.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.108 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.108.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.108 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.108.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.108 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.108.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.108 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.108.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.109.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.109.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.109 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.109.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.109 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.109.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.109 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.109.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.109 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.109.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.109 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.109.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.109 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.109.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.109 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.109.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.109 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.109.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.109 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.109.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.109 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/10/PGA_scaffold34__164_contigs__length_87950420.109.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.110.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.110.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.110 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.110.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.110 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.110.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.110 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.110.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.110 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.110.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.110 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.110.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.110 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.110.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.110 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.110.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.110 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.110.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.110 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.110.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.110 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.110.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.111.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.111.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.111 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.111.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.111 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.111.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.111 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.111.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.111 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.111.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.111 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.111.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.111 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.111.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.111 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.111.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.111 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.111.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.111 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.111.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.111 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.111.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.112.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.112.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.112 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.112.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.112 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.112.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.112 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.112.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.112 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.112.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.112 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.112.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.112 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.112.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.112 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.112.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.112 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.112.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.112 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.112.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.112 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.112.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.113.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.113.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.113 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.113.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.113 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.113.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.113 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.113.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.113 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.113.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.113 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.113.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.113 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.113.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.113 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.113.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.113 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.113.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.113 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.113.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.113 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.113.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.114.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.114.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.114 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.114.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.114 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.114.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.114 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.114.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.114 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.114.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.114 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.114.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.114 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.114.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.114 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.114.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.114 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.114.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.114 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.114.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.114 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.114.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.115.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.115.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.115 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.115.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.115 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.115.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.115 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.115.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.115 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.115.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.115 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.115.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.115 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.115.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.115 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.115.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.115 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.115.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.115 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.115.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.115 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.115.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.116.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.116.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.116 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.116.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.116 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.116.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.116 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.116.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.116 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.116.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.116 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.116.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.116 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.116.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.116 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.116.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.116 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.116.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.116 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.116.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.116 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.116.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.117.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.117.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.117 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.117.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.117 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.117.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.117 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.117.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.117 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.117.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.117 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.117.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.117 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.117.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.117 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.117.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.117 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.117.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.117 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.117.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.117 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.117.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.118.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.118.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.118 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.118.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.118 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.118.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.118 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.118.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.118 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.118.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.118 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.118.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.118 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.118.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.118 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.118.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.118 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.118.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.118 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.118.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.118 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.118.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.119.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.119.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.119 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.119.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.119 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.119.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.119 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.119.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.119 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.119.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.119 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.119.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.119 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.119.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.119 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.119.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.119 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.119.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.119 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.119.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.119 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/11/PGA_scaffold34__164_contigs__length_87950420.119.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:3 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.120.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.120.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.120 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.120.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.120 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.120.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.120 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.120.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.120 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.120.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.120 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.120.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.120 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.120.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.120 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.120.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.120 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.120.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.120 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.120.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.120 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.120.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.121.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.121.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.121 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.121.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.121 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.121.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.121 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.121.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.121 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.121.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.121 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.121.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.121 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.121.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.121 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.121.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.121 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.121.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.121 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.121.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.121 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.121.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.122.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.122.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.122 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.122.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.122 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.122.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.122 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.122.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.122 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.122.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.122 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.122.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.122 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.122.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.122 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.122.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.122 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.122.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.122 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.122.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.122 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.122.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.123.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.123.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.123 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.123.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.123 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.123.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.123 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.123.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.123 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.123.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.123 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.123.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.123 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.123.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.123 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.123.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.123 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.123.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.123 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.123.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.123 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.123.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.124.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.124.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.124 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.124.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.124 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.124.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.124 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.124.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.124 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.124.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.124 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.124.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.124 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.124.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.124 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.124.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.124 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.124.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.124 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.124.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.124 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.124.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.125.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.125.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.125 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.125.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.125 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.125.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.125 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.125.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.125 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.125.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.125 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.125.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.125 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.125.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.125 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.125.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.125 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.125.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.125 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.125.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.125 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.125.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.126.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.126.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.126 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.126.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.126 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.126.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.126 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.126.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.126 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.126.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.126 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.126.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.126 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.126.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.126 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.126.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.126 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.126.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.126 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.126.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.126 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.126.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.127.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.127.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.127 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.127.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.127 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.127.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.127 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.127.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.127 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.127.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.127 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.127.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.127 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.127.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.127 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.127.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.127 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.127.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.127 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.127.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.127 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.127.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.128.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.128.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.128 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.128.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.128 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.128.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.128 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.128.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.128 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.128.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.128 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.128.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.128 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.128.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.128 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.128.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.128 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.128.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.128 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.128.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.128 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.128.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.129.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.129.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.129 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.129.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.129 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.129.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.129 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.129.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.129 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.129.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.129 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.129.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.129 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.129.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.129 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.129.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.129 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.129.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.129 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.129.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.129 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/12/PGA_scaffold34__164_contigs__length_87950420.129.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.130.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.130.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.130 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.130.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.130 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.130.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.130 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.130.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.130 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.130.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.130 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.130.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.130 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.130.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.130 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.130.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.130 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.130.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.130 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.130.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.130 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.130.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.131.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.131.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.131 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.131.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.131 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.131.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.131 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.131.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.131 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.131.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.131 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.131.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.131 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.131.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.131 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.131.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.131 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.131.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.131 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.131.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.131 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.131.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.132.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.132.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.132 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.132.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.132 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.132.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.132 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.132.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.132 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.132.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.132 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.132.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.132 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.132.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.132 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.132.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.132 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.132.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.132 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.132.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.132 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.132.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.133.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.133.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.133 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.133.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.133 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.133.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.133 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.133.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.133 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.133.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.133 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.133.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.133 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.133.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.133 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.133.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.133 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.133.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.133 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.133.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.133 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.133.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:2 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.134.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.134.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.134 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.134.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.134 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.134.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.134 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.134.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.134 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.134.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.134 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.134.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.134 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.134.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.134 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.134.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.134 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.134.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.134 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.134.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.134 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.134.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.135.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.135.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.135 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.135.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.135 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.135.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.135 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.135.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.135 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.135.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.135 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.135.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.135 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.135.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.135 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.135.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.135 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.135.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.135 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.135.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.135 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.135.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.136.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.136.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.136 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.136.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.136 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.136.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.136 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.136.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.136 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.136.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.136 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.136.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.136 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.136.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.136 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.136.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.136 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.136.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.136 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.136.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.136 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.136.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.137.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.137.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.137 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.137.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.137 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.137.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.137 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.137.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.137 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.137.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.137 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.137.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.137 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.137.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.137 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.137.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.137 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.137.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.137 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.137.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.137 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.137.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.138.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.138.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.138 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.138.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.138 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.138.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.138 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.138.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.138 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.138.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.138 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.138.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.138 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.138.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.138 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.138.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.138 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.138.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.138 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.138.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.138 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.138.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.139.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.139.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.139 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.139.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.139 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.139.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.139 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.139.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.139 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.139.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.139 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.139.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.139 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.139.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.139 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.139.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.139 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.139.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.139 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.139.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.139 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/13/PGA_scaffold34__164_contigs__length_87950420.139.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.140.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.140.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.140 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.140.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.140 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.140.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.140 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.140.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.140 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.140.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.140 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.140.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.140 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.140.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.140 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.140.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.140 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.140.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.140 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.140.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.140 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.140.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.141.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.141.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.141 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.141.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.141 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.141.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.141 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.141.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.141 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.141.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.141 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.141.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.141 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.141.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.141 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.141.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.141 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.141.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.141 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.141.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.141 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.141.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.142.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.142.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.142 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.142.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.142 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.142.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.142 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.142.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.142 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.142.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.142 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.142.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.142 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.142.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.142 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.142.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.142 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.142.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.142 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.142.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.142 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.142.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.143.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.143.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.143 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.143.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.143 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.143.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:10 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.143 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.143.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.143 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.143.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.143 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.143.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:10 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.143 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.143.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.143 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.143.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:8 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.143 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.143.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.143 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.143.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.143 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.143.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:6 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.144.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.144.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.144 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.144.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.144 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.144.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:8 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.144 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.144.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.144 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.144.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.144 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.144.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.144 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.144.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.144 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.144.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.144 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.144.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.144 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.144.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.144 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.144.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:3 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.145.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.145.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.145 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.145.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.145 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.145.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.145 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.145.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.145 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.145.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.145 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.145.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.145 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.145.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.145 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.145.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.145 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.145.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.145 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.145.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.145 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.145.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.146.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.146.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.146 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.146.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.146 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.146.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.146 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.146.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.146 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.146.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.146 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.146.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.146 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.146.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.146 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.146.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.146 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.146.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.146 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.146.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.146 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.146.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.147.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.147.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.147 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.147.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.147 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.147.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.147 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.147.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.147 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.147.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.147 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.147.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.147 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.147.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.147 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.147.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.147 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.147.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.147 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.147.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.147 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.147.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.148.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.148.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.148 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.148.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.148 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.148.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.148 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.148.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.148 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.148.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.148 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.148.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.148 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.148.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.148 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.148.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.148 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.148.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.148 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.148.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.148 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.148.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.149.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.149.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.149 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.149.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.149 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.149.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.149 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.149.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.149 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.149.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.149 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.149.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.149 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.149.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.149 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.149.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.149 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.149.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.149 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.149.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.149 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/14/PGA_scaffold34__164_contigs__length_87950420.149.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.150.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.150.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.150 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.150.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.150 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.150.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.150 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.150.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.150 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.150.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.150 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.150.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.150 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.150.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.150 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.150.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.150 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.150.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.150 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.150.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.150 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.150.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.151.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.151.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.151 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.151.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.151 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.151.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.151 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.151.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.151 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.151.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.151 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.151.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.151 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.151.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.151 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.151.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.151 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.151.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.151 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.151.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.151 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.151.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.152.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.152.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.152 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.152.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.152 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.152.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.152 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.152.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.152 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.152.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.152 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.152.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.152 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.152.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.152 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.152.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.152 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.152.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.152 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.152.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.152 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.152.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.153.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.153.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.153 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.153.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.153 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.153.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.153 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.153.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.153 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.153.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.153 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.153.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.153 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.153.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.153 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.153.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.153 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.153.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.153 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.153.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.153 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.153.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.154.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.154.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.154 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.154.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.154 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.154.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.154 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.154.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.154 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.154.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.154 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.154.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.154 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.154.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.154 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.154.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.154 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.154.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.154 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.154.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.154 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.154.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.155.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.155.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.155 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.155.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.155 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.155.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.155 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.155.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.155 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.155.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.155 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.155.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.155 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.155.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.155 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.155.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.155 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.155.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.155 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.155.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.155 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.155.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.156.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.156.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.156 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.156.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.156 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.156.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.156 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.156.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.156 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.156.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.156 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.156.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.156 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.156.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.156 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.156.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.156 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.156.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.156 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.156.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.156 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.156.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.157.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.157.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.157 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.157.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.157 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.157.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.157 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.157.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.157 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.157.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.157 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.157.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.157 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.157.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.157 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.157.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.157 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.157.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.157 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.157.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.157 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.157.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.158.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.158.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.158 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.158.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.158 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.158.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.158 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.158.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.158 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.158.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.158 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.158.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.158 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.158.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.158 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.158.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.158 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.158.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.158 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.158.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.158 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.158.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.159.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.159.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.159 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.159.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.159 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.159.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.159 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.159.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.159 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.159.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.159 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.159.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.159 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.159.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.159 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.159.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.159 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.159.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.159 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.159.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.159 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/15/PGA_scaffold34__164_contigs__length_87950420.159.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.160.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.160.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.160 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.160.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.160 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.160.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.160 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.160.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.160 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.160.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.160 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.160.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.160 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.160.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.160 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.160.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.160 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.160.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.160 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.160.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.160 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.160.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.161.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.161.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.161 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.161.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:75 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.161 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.161.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:53 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.161 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.161.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:43 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.161 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.161.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:57 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.161 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.161.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:56 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.161 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.161.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:71 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.161 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.161.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:46 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.161 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.161.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:58 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.161 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.161.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:61 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.161 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.161.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:54 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.162.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.162.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.162 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.162.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.162 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.162.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.162 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.162.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.162 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.162.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.162 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.162.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.162 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.162.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.162 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.162.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.162 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.162.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.162 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.162.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.162 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.162.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.163.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.163.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.163 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.163.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.163 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.163.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.163 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.163.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.163 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.163.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.163 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.163.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.163 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.163.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.163 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.163.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.163 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.163.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.163 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.163.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.163 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.163.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.164.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.164.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.164 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.164.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.164 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.164.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.164 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.164.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.164 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.164.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.164 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.164.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.164 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.164.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.164 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.164.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.164 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.164.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.164 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.164.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.164 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.164.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:3 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.165.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.165.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.165 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.165.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.165 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.165.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.165 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.165.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.165 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.165.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.165 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.165.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.165 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.165.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.165 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.165.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.165 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.165.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.165 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.165.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.165 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.165.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.166.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.166.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.166 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.166.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.166 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.166.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.166 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.166.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.166 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.166.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.166 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.166.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.166 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.166.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.166 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.166.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.166 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.166.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.166 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.166.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.166 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.166.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.167.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.167.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.167 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.167.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.167 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.167.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.167 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.167.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.167 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.167.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.167 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.167.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.167 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.167.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.167 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.167.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.167 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.167.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.167 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.167.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.167 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.167.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.168.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.168.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.168 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.168.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.168 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.168.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.168 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.168.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.168 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.168.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.168 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.168.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.168 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.168.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.168 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.168.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.168 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.168.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.168 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.168.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.168 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.168.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.169.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.169.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.169 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.169.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.169 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.169.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.169 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.169.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.169 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.169.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.169 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.169.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.169 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.169.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.169 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.169.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.169 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.169.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.169 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.169.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.169 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/16/PGA_scaffold34__164_contigs__length_87950420.169.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.170.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.170.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.170 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.170.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.170 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.170.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.170 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.170.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.170 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.170.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.170 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.170.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.170 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.170.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.170 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.170.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.170 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.170.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.170 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.170.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.170 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.170.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.171.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.171.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.171 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.171.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.171 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.171.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.171 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.171.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.171 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.171.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.171 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.171.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.171 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.171.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.171 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.171.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.171 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.171.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.171 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.171.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.171 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.171.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.172.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.172.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.172 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.172.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.172 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.172.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.172 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.172.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.172 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.172.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.172 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.172.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.172 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.172.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.172 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.172.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.172 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.172.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.172 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.172.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.172 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.172.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.173.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.173.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.173 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.173.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.173 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.173.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.173 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.173.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.173 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.173.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.173 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.173.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.173 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.173.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.173 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.173.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.173 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.173.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.173 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.173.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.173 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.173.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.174.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.174.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.174 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.174.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.174 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.174.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.174 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.174.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.174 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.174.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.174 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.174.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.174 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.174.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.174 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.174.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.174 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.174.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.174 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.174.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.174 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.174.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.175.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.175.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.175 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.175.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.175 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.175.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.175 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.175.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.175 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.175.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.175 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.175.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.175 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.175.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.175 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.175.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.175 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.175.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.175 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.175.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.175 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.175.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.176.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.176.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.176 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.176.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.176 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.176.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.176 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.176.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.176 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.176.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.176 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.176.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.176 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.176.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.176 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.176.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.176 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.176.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.176 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.176.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.176 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.176.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.177.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.177.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.177 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.177.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.177 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.177.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.177 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.177.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.177 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.177.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.177 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.177.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.177 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.177.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.177 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.177.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.177 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.177.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.177 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.177.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.177 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.177.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.178.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.178.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.178 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.178.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.178 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.178.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.178 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.178.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.178 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.178.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.178 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.178.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.178 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.178.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.178 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.178.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.178 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.178.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.178 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.178.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.178 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.178.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.179.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.179.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.179 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.179.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.179 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.179.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.179 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.179.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.179 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.179.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.179 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.179.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.179 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.179.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.179 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.179.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.179 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.179.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.179 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.179.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.179 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/17/PGA_scaffold34__164_contigs__length_87950420.179.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.180.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.180.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.180 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.180.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.180 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.180.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.180 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.180.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.180 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.180.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.180 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.180.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.180 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.180.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.180 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.180.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.180 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.180.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.180 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.180.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.180 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.180.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.181.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.181.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.181 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.181.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:14 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.181 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.181.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:17 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.181 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.181.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.181 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.181.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:15 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.181 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.181.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:16 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.181 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.181.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:13 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.181 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.181.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:13 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.181 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.181.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:14 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.181 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.181.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.181 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.181.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:10 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.182.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.182.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.182 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.182.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.182 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.182.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.182 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.182.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.182 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.182.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.182 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.182.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.182 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.182.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.182 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.182.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.182 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.182.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.182 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.182.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.182 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.182.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.183.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.183.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.183 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.183.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.183 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.183.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.183 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.183.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.183 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.183.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.183 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.183.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.183 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.183.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.183 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.183.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.183 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.183.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.183 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.183.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.183 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.183.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.184.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.184.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.184 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.184.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.184 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.184.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.184 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.184.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.184 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.184.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.184 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.184.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.184 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.184.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.184 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.184.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.184 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.184.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.184 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.184.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.184 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.184.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.185.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.185.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.185 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.185.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.185 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.185.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.185 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.185.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.185 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.185.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.185 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.185.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.185 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.185.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.185 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.185.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.185 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.185.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.185 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.185.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.185 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.185.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.186.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.186.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.186 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.186.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.186 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.186.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.186 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.186.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.186 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.186.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.186 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.186.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.186 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.186.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.186 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.186.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.186 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.186.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.186 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.186.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.186 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.186.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.187.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.187.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.187 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.187.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.187 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.187.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.187 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.187.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.187 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.187.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.187 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.187.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.187 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.187.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.187 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.187.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.187 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.187.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.187 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.187.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.187 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.187.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.188.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.188.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.188 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.188.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.188 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.188.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.188 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.188.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.188 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.188.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.188 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.188.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.188 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.188.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.188 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.188.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.188 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.188.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.188 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.188.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.188 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.188.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.189.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.189.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.189 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.189.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.189 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.189.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.189 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.189.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.189 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.189.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.189 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.189.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.189 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.189.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.189 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.189.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.189 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.189.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.189 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.189.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.189 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/18/PGA_scaffold34__164_contigs__length_87950420.189.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.190.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.190.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.190 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.190.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.190 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.190.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.190 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.190.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.190 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.190.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.190 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.190.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.190 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.190.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.190 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.190.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.190 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.190.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.190 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.190.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.190 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.190.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.191.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.191.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.191 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.191.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.191 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.191.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.191 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.191.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.191 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.191.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.191 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.191.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.191 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.191.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.191 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.191.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.191 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.191.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.191 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.191.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.191 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.191.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.192.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.192.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.192 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.192.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.192 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.192.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.192 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.192.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.192 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.192.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.192 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.192.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:8 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.192 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.192.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.192 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.192.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:8 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.192 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.192.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.192 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.192.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:8 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.192 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.192.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:4 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.193.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.193.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.193 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.193.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.193 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.193.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.193 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.193.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.193 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.193.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.193 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.193.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.193 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.193.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.193 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.193.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.193 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.193.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.193 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.193.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.193 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.193.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.194.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.194.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.194 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.194.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.194 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.194.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.194 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.194.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.194 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.194.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.194 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.194.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.194 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.194.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.194 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.194.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.194 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.194.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.194 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.194.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.194 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.194.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.195.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.195.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.195 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.195.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.195 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.195.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.195 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.195.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.195 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.195.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.195 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.195.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.195 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.195.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.195 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.195.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.195 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.195.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.195 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.195.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.195 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.195.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.196.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.196.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.196 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.196.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.196 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.196.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.196 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.196.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.196 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.196.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.196 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.196.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.196 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.196.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.196 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.196.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.196 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.196.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.196 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.196.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.196 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.196.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.197.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.197.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.197 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.197.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.197 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.197.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.197 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.197.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.197 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.197.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.197 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.197.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.197 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.197.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.197 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.197.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.197 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.197.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.197 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.197.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.197 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.197.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.198.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.198.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.198 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.198.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.198 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.198.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.198 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.198.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.198 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.198.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.198 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.198.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.198 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.198.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.198 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.198.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.198 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.198.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.198 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.198.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.198 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.198.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.199.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.199.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.199 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.199.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:15 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.199 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.199.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.199 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.199.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.199 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.199.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:12 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.199 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.199.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:10 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.199 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.199.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:11 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.199 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.199.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.199 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.199.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:12 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.199 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.199.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.199 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/19/PGA_scaffold34__164_contigs__length_87950420.199.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:4 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.200.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.200.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.200 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.200.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.200 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.200.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.200 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.200.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.200 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.200.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.200 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.200.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.200 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.200.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.200 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.200.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.200 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.200.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.200 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.200.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.200 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.200.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.201.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.201.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.201 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.201.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.201 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.201.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.201 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.201.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.201 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.201.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.201 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.201.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.201 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.201.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.201 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.201.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.201 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.201.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.201 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.201.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.201 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.201.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.202.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.202.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.202 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.202.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.202 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.202.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.202 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.202.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.202 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.202.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.202 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.202.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.202 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.202.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.202 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.202.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.202 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.202.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.202 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.202.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.202 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.202.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.203.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.203.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.203 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.203.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.203 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.203.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.203 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.203.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.203 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.203.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.203 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.203.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.203 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.203.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.203 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.203.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.203 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.203.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.203 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.203.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.203 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.203.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.204.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.204.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.204 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.204.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.204 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.204.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.204 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.204.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.204 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.204.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.204 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.204.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.204 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.204.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.204 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.204.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.204 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.204.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.204 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.204.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.204 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.204.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.205.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.205.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.205 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.205.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.205 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.205.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.205 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.205.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.205 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.205.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.205 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.205.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.205 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.205.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.205 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.205.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.205 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.205.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.205 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.205.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.205 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.205.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.206.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.206.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.206 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.206.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.206 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.206.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.206 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.206.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.206 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.206.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.206 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.206.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.206 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.206.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.206 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.206.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.206 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.206.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.206 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.206.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.206 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.206.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.207.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.207.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.207 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.207.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.207 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.207.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.207 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.207.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.207 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.207.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.207 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.207.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.207 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.207.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.207 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.207.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.207 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.207.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.207 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.207.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.207 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.207.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.208.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.208.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.208 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.208.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.208 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.208.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.208 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.208.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.208 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.208.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.208 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.208.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.208 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.208.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.208 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.208.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.208 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.208.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.208 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.208.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.208 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.208.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.209.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.209.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.209 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.209.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.209 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.209.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.209 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.209.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.209 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.209.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.209 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.209.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.209 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.209.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.209 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.209.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.209 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.209.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.209 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.209.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.209 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/20/PGA_scaffold34__164_contigs__length_87950420.209.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.210.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.210.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.210 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.210.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.210 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.210.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.210 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.210.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.210 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.210.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.210 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.210.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.210 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.210.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.210 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.210.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.210 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.210.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.210 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.210.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.210 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.210.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.211.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.211.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.211 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.211.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.211 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.211.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.211 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.211.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.211 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.211.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.211 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.211.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.211 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.211.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.211 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.211.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.211 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.211.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.211 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.211.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.211 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.211.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.212.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.212.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.212 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.212.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.212 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.212.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.212 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.212.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.212 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.212.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.212 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.212.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.212 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.212.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.212 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.212.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.212 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.212.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.212 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.212.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.212 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.212.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.213.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.213.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.213 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.213.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.213 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.213.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.213 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.213.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.213 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.213.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.213 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.213.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.213 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.213.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.213 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.213.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.213 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.213.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.213 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.213.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.213 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.213.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.214.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.214.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.214 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.214.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.214 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.214.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.214 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.214.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.214 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.214.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.214 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.214.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.214 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.214.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.214 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.214.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.214 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.214.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.214 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.214.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.214 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.214.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.215.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.215.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.215 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.215.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.215 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.215.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.215 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.215.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.215 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.215.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.215 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.215.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.215 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.215.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.215 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.215.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.215 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.215.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.215 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.215.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.215 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.215.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.216.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.216.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.216 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.216.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.216 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.216.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.216 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.216.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.216 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.216.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.216 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.216.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.216 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.216.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.216 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.216.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.216 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.216.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.216 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.216.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.216 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.216.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:2 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.217.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.217.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.217 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.217.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.217 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.217.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.217 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.217.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.217 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.217.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.217 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.217.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.217 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.217.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.217 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.217.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.217 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.217.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.217 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.217.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.217 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.217.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.218.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.218.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.218 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.218.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.218 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.218.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.218 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.218.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.218 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.218.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.218 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.218.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.218 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.218.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.218 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.218.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.218 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.218.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.218 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.218.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.218 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.218.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.219.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.219.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.219 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.219.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.219 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.219.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.219 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.219.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.219 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.219.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.219 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.219.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.219 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.219.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.219 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.219.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.219 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.219.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.219 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.219.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.219 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/21/PGA_scaffold34__164_contigs__length_87950420.219.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:2 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.220.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.220.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.220 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.220.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:41 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.220 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.220.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:28 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.220 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.220.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:24 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.220 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.220.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:24 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.220 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.220.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:27 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.220 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.220.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:40 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.220 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.220.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:25 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.220 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.220.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:31 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.220 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.220.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:37 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.220 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.220.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:26 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.221.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.221.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.221 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.221.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.221 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.221.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.221 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.221.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.221 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.221.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.221 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.221.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.221 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.221.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.221 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.221.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.221 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.221.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.221 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.221.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.221 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.221.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.222.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.222.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.222 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.222.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.222 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.222.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.222 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.222.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.222 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.222.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.222 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.222.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.222 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.222.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.222 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.222.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.222 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.222.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.222 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.222.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.222 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.222.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.223.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.223.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.223 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.223.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.223 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.223.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.223 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.223.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.223 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.223.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.223 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.223.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.223 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.223.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.223 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.223.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.223 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.223.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.223 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.223.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.223 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.223.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.224.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.224.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.224 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.224.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.224 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.224.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.224 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.224.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.224 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.224.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.224 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.224.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.224 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.224.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.224 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.224.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.224 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.224.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.224 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.224.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.224 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.224.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.225.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.225.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.225 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.225.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.226.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.226.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.226 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.226.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.227.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.227.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.227 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.227.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.227 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.227.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.227 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.227.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.227 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.227.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.227 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.227.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.227 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.227.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.227 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.227.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.227 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.227.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.227 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.227.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.227 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.227.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.228.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.228.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.228 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.228.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.228 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.228.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.228 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.228.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.228 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.228.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.228 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.228.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.228 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.228.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.228 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.228.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.228 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.228.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.228 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.228.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.228 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.228.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.229.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.229.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.229 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.229.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.229 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.229.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.229 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.229.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.229 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.229.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.229 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.229.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.229 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.229.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.229 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.229.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.229 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.229.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.229 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.229.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.229 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/22/PGA_scaffold34__164_contigs__length_87950420.229.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.230.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.230.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.230 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.230.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.230 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.230.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.230 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.230.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.230 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.230.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.230 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.230.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.230 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.230.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.230 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.230.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.230 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.230.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.230 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.230.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.230 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.230.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.231.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.231.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.231 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.231.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.231 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.231.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.231 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.231.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.231 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.231.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.231 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.231.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.231 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.231.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.231 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.231.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.231 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.231.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.231 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.231.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.231 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.231.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.232.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.232.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.232 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.232.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.232 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.232.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.232 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.232.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.232 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.232.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.232 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.232.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.232 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.232.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.232 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.232.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.232 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.232.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.232 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.232.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.232 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.232.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.233.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.233.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.233 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.233.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.233 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.233.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.233 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.233.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.233 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.233.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.233 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.233.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.233 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.233.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.233 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.233.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.233 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.233.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.233 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.233.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.233 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.233.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.234.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.234.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.234 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.234.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.234 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.234.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.234 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.234.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.234 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.234.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.234 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.234.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.234 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.234.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.234 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.234.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.234 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.234.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.234 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.234.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.234 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.234.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.235.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.235.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.235 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.235.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.235 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.235.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.235 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.235.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.235 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.235.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.235 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.235.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.235 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.235.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.235 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.235.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.235 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.235.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.235 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.235.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.235 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.235.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.236.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.236.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.236 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.236.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:69 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.236 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.236.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:37 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.236 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.236.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:31 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.236 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.236.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:46 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.236 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.236.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:50 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.236 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.236.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:65 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.236 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.236.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:43 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.236 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.236.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:51 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.236 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.236.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:51 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.236 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.236.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:49 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.237.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.237.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.237 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.237.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.237 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.237.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.237 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.237.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.237 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.237.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.237 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.237.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.237 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.237.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.237 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.237.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.237 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.237.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.237 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.237.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.237 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.237.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.238.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.238.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.238 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.238.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.238 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.238.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.238 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.238.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.238 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.238.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.238 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.238.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.238 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.238.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.238 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.238.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.238 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.238.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.238 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.238.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.238 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.238.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.239.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.239.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.239 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.239.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.239 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.239.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.239 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.239.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.239 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.239.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.239 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.239.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.239 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.239.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.239 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.239.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.239 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.239.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.239 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.239.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.239 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/23/PGA_scaffold34__164_contigs__length_87950420.239.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.240.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.240.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.240 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.240.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.240 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.240.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.240 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.240.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.240 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.240.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.240 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.240.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.240 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.240.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.240 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.240.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.240 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.240.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.240 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.240.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.240 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.240.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.241.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.241.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.241 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.241.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.241 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.241.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.241 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.241.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.241 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.241.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.241 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.241.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.241 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.241.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.241 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.241.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.241 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.241.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.241 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.241.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.241 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.241.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.242.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.242.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.242 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.242.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.242 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.242.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.242 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.242.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.242 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.242.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.242 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.242.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.242 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.242.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.242 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.242.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.242 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.242.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.242 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.242.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.242 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.242.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.243.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.243.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.243 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.243.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.243 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.243.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.243 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.243.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.243 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.243.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.243 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.243.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.243 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.243.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.243 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.243.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.243 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.243.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.243 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.243.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.243 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.243.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.244.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.244.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.244 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.244.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.244 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.244.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.244 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.244.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.244 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.244.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.244 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.244.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.244 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.244.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.244 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.244.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.244 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.244.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.244 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.244.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.244 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.244.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.245.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.245.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.245 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.245.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.245 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.245.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.245 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.245.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.245 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.245.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.245 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.245.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.245 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.245.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.245 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.245.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.245 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.245.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.245 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.245.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.245 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.245.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.246.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.246.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.246 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.246.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.246 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.246.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.246 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.246.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.246 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.246.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.246 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.246.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.246 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.246.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.246 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.246.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.246 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.246.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.246 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.246.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.246 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.246.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.247.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.247.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.247 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.247.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.247 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.247.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.247 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.247.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.247 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.247.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.247 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.247.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.247 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.247.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.247 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.247.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.247 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.247.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.247 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.247.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.247 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.247.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.248.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.248.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.248 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.248.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.248 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.248.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.248 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.248.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.248 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.248.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.248 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.248.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.248 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.248.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.248 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.248.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.248 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.248.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.248 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.248.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.248 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.248.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.249.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.249.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.249 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.249.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.249 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.249.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.249 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.249.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.249 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.249.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.249 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.249.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.249 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.249.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.249 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.249.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.249 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.249.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.249 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.249.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.249 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/24/PGA_scaffold34__164_contigs__length_87950420.249.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.250.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.250.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.250 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.250.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.250 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.250.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.250 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.250.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.250 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.250.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.250 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.250.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.250 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.250.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.250 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.250.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.250 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.250.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.250 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.250.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.250 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.250.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.251.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.251.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.251 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.251.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.251 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.251.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.251 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.251.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.251 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.251.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.251 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.251.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.251 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.251.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.251 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.251.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.251 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.251.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.251 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.251.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.251 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.251.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.252.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.252.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.252 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.252.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.252 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.252.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.252 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.252.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.252 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.252.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.252 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.252.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.252 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.252.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.252 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.252.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.252 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.252.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.252 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.252.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.252 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.252.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.253.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.253.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.253 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.253.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.253 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.253.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.253 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.253.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.253 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.253.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.253 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.253.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.253 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.253.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.253 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.253.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.253 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.253.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.253 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.253.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.253 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.253.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:4 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.254.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.254.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.254 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.254.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.254 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.254.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.254 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.254.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.254 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.254.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.254 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.254.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.254 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.254.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.254 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.254.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.254 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.254.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.254 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.254.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.254 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.254.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.255.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.255.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.255 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.255.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.255 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.255.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.255 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.255.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.255 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.255.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.255 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.255.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.255 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.255.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.255 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.255.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.255 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.255.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.255 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.255.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.255 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.255.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.256.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.256.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.256 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.256.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.256 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.256.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.256 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.256.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.256 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.256.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.256 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.256.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.256 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.256.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.256 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.256.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.256 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.256.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.256 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.256.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.256 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.256.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.257.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.257.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.257 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.257.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.257 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.257.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.257 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.257.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.257 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.257.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.257 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.257.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.257 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.257.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.257 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.257.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.257 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.257.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.257 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.257.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.257 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.257.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.258.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.258.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.258 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.258.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:11 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.258 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.258.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:14 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.258 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.258.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.258 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.258.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:17 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.258 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.258.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:17 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.258 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.258.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:11 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.258 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.258.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:15 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.258 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.258.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:11 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.258 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.258.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:12 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.258 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.258.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:11 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.259.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.259.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.259 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.259.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.259 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.259.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.259 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.259.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.259 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.259.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.259 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.259.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.259 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.259.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.259 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.259.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.259 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.259.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.259 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.259.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.259 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/25/PGA_scaffold34__164_contigs__length_87950420.259.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.260.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.260.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.260 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.260.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.260 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.260.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.260 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.260.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.260 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.260.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.260 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.260.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.260 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.260.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.260 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.260.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.260 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.260.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.260 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.260.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.260 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.260.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.261.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.261.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.261 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.261.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.261 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.261.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.261 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.261.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.261 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.261.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.261 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.261.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.261 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.261.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.261 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.261.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.261 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.261.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.261 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.261.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.261 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.261.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.262.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.262.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.262 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.262.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.262 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.262.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.262 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.262.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.262 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.262.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.262 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.262.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.262 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.262.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.262 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.262.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.262 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.262.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.262 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.262.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.262 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.262.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.263.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.263.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.263 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.263.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.263 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.263.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.263 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.263.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.263 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.263.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.263 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.263.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.263 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.263.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.263 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.263.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.263 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.263.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.263 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.263.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.263 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.263.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.264.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.264.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.264 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.264.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:33 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.264 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.264.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:21 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.264 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.264.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:15 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.264 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.264.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:13 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.264 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.264.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:16 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.264 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.264.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:20 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.264 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.264.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:15 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.264 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.264.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:15 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.264 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.264.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:14 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.264 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.264.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:23 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.265.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.265.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.265 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.265.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.265 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.265.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.265 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.265.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.265 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.265.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.265 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.265.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.265 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.265.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.265 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.265.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.265 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.265.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.265 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.265.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.265 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.265.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.266.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.266.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.266 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.266.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.266 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.266.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.266 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.266.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.266 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.266.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.266 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.266.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.266 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.266.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.266 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.266.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.266 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.266.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.266 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.266.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.266 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.266.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.267.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.267.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.267 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.267.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.267 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.267.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.267 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.267.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.267 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.267.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.267 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.267.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.267 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.267.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.267 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.267.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.267 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.267.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.267 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.267.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.267 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.267.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.268.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.268.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.268 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.268.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.268 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.268.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.268 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.268.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.268 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.268.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.268 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.268.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.268 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.268.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.268 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.268.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.268 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.268.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.268 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.268.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.268 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.268.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.269.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.269.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.269 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.269.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.269 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.269.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.269 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.269.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.269 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.269.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.269 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.269.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.269 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.269.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.269 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.269.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.269 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.269.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.269 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.269.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.269 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/26/PGA_scaffold34__164_contigs__length_87950420.269.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.270.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.270.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.270 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.270.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.270 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.270.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.270 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.270.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.270 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.270.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.270 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.270.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.270 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.270.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.270 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.270.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.270 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.270.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.270 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.270.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.270 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.270.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.271.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.271.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.271 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.271.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.271 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.271.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.271 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.271.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.271 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.271.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.271 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.271.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.271 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.271.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.271 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.271.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.271 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.271.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.271 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.271.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.271 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.271.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.272.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.272.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.272 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.272.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.272 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.272.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.272 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.272.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.272 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.272.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.272 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.272.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.272 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.272.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.272 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.272.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.272 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.272.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.272 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.272.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.272 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.272.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:2 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.273.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.273.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.273 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.273.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.273 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.273.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.273 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.273.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.273 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.273.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.273 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.273.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.273 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.273.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.273 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.273.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.273 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.273.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.273 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.273.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.273 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.273.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.274.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.274.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.274 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.274.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.274 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.274.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.274 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.274.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.274 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.274.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.274 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.274.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.274 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.274.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.274 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.274.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.274 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.274.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.274 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.274.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.274 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.274.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.275.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.275.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.275 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.275.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.275 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.275.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.275 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.275.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.275 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.275.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.275 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.275.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.275 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.275.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.275 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.275.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.275 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.275.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.275 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.275.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.275 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.275.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.276.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.276.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.276 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.276.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:77 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.276 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.276.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:51 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.276 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.276.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:35 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.276 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.276.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:44 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.276 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.276.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:50 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.276 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.276.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:59 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.276 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.276.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:40 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.276 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.276.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:53 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.276 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.276.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:63 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.276 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.276.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:46 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.277.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.277.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.277 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.277.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.277 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.277.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.277 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.277.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.277 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.277.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.277 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.277.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.277 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.277.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.277 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.277.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.277 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.277.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.277 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.277.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.277 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.277.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.278.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.278.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.278 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.278.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.278 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.278.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.278 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.278.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.278 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.278.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.278 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.278.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.278 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.278.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.278 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.278.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.278 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.278.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.278 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.278.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.278 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.278.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.279.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.279.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.279 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.279.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.279 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.279.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.279 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.279.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.279 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.279.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.279 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.279.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.279 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.279.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.279 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.279.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.279 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.279.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.279 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.279.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.279 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/27/PGA_scaffold34__164_contigs__length_87950420.279.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.280.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.280.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.280 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.280.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.280 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.280.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.280 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.280.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.280 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.280.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.280 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.280.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.280 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.280.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.280 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.280.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.280 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.280.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.280 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.280.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.280 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.280.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.281.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.281.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.281 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.281.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.281 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.281.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.281 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.281.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.281 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.281.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.281 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.281.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.281 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.281.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.281 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.281.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.281 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.281.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.281 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.281.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.281 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.281.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.282.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.282.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.282 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.282.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.282 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.282.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.282 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.282.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.282 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.282.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.282 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.282.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.282 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.282.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.282 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.282.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.282 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.282.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.282 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.282.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.282 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.282.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.283.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.283.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.283 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.283.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.283 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.283.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.283 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.283.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.283 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.283.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.283 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.283.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.283 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.283.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.283 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.283.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.283 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.283.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.283 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.283.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.283 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.283.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.284.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.284.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.284 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.284.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.284 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.284.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.284 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.284.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.284 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.284.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.284 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.284.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.284 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.284.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.284 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.284.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.284 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.284.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.284 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.284.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.284 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.284.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.285.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.285.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.285 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.285.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.285 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.285.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.285 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.285.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.285 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.285.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.285 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.285.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.285 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.285.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.285 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.285.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.285 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.285.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.285 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.285.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.285 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.285.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.286.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.286.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.286 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.286.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.286 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.286.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.286 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.286.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.286 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.286.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.286 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.286.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.286 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.286.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.286 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.286.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.286 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.286.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.286 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.286.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.286 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.286.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.287.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.287.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.287 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.287.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.287 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.287.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.287 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.287.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.287 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.287.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.287 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.287.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.287 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.287.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.287 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.287.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.287 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.287.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.287 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.287.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.287 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.287.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.288.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.288.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.288 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.288.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.288 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.288.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.288 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.288.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.288 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.288.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.288 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.288.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.288 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.288.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.288 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.288.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.288 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.288.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.288 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.288.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.288 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.288.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.289.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.289.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.289 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.289.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.289 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.289.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.289 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.289.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.289 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.289.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.289 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.289.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.289 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.289.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.289 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.289.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.289 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.289.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.289 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.289.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.289 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/28/PGA_scaffold34__164_contigs__length_87950420.289.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.290.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.290.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.290 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.290.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.290 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.290.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.290 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.290.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.290 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.290.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.290 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.290.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.290 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.290.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.290 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.290.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.290 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.290.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.290 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.290.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.290 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.290.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.291.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.291.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.291 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.291.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.291 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.291.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.291 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.291.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.291 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.291.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.291 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.291.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.291 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.291.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.291 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.291.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.291 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.291.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.291 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.291.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.291 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.291.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.292.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.292.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.292 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.292.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.292 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.292.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.292 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.292.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.292 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.292.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.292 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.292.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.292 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.292.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.292 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.292.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.292 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.292.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.292 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.292.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.292 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.292.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.293.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.293.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.293 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.293.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.293 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.293.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.293 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.293.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.293 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.293.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.293 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.293.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.293 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.293.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.293 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.293.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.293 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.293.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.293 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.293.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.293 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.293.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.294.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.294.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.294 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.294.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.294 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.294.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.294 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.294.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.294 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.294.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.294 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.294.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.294 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.294.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.294 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.294.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.294 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.294.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.294 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.294.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.294 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.294.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.295.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.295.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.295 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.295.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.295 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.295.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.295 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.295.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.295 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.295.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.295 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.295.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.295 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.295.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.295 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.295.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.295 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.295.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.295 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.295.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.295 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.295.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.296.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.296.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.296 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.296.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.296 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.296.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.296 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.296.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.296 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.296.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.296 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.296.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.296 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.296.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.296 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.296.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.296 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.296.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.296 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.296.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.296 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.296.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.297.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.297.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.297 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.297.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.297 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.297.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.297 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.297.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.297 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.297.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.297 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.297.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.297 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.297.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.297 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.297.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.297 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.297.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.297 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.297.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.297 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.297.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.298.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.298.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.298 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.298.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.298 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.298.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.298 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.298.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.298 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.298.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.298 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.298.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.298 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.298.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.298 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.298.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.298 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.298.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.298 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.298.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.298 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.298.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.299.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.299.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.299 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.299.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.299 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.299.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.299 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.299.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.299 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.299.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.299 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.299.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.299 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.299.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.299 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.299.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.299 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.299.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.299 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.299.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.299 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/29/PGA_scaffold34__164_contigs__length_87950420.299.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.300.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.300.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.300 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.300.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.300 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.300.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.300 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.300.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.300 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.300.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.300 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.300.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.300 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.300.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.300 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.300.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.300 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.300.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.300 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.300.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.300 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.300.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.301.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.301.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.301 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.301.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.301 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.301.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.301 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.301.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.301 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.301.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.301 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.301.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.301 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.301.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.301 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.301.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.301 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.301.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.301 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.301.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.301 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.301.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.302.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.302.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.302 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.302.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.302 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.302.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.302 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.302.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.302 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.302.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.302 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.302.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.302 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.302.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.302 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.302.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.302 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.302.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.302 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.302.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.302 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.302.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.303.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.303.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.303 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.303.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.303 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.303.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.303 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.303.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.303 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.303.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.303 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.303.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.303 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.303.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.303 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.303.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.303 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.303.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.303 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.303.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.303 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.303.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.304.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.304.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.304 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.304.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.304 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.304.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.304 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.304.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.304 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.304.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.304 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.304.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.304 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.304.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.304 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.304.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.304 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.304.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.304 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.304.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.304 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.304.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.305.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.305.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.305 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.305.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.305 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.305.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.305 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.305.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.305 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.305.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.305 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.305.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.305 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.305.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.305 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.305.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.305 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.305.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.305 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.305.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.305 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.305.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.306.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.306.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.306 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.306.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.306 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.306.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.306 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.306.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.306 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.306.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.306 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.306.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.306 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.306.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.306 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.306.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.306 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.306.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.306 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.306.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.306 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.306.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.307.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.307.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.307 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.307.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.307 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.307.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.307 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.307.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.307 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.307.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.307 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.307.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.307 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.307.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.307 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.307.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.307 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.307.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.307 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.307.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.307 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.307.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.308.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.308.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.308 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.308.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.308 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.308.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.308 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.308.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.308 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.308.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.308 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.308.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.308 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.308.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.308 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.308.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.308 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.308.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.308 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.308.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.308 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.308.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.309.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.309.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.309 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.309.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:999 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.309 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.309.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:963 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.309 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.309.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:997 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.309 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.309.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:988 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.309 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.309.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:973 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.309 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.309.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1022 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.309 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.309.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:996 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.309 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.309.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1042 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.309 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.309.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:986 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.309 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/30/PGA_scaffold34__164_contigs__length_87950420.309.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1001 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.310.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.310.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.310 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.310.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.310 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.310.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.310 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.310.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.310 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.310.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.310 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.310.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.310 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.310.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.310 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.310.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.310 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.310.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.310 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.310.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.310 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.310.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.311.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.311.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.311 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.311.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.311 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.311.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.311 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.311.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.311 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.311.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.311 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.311.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.311 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.311.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.311 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.311.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.311 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.311.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.311 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.311.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.311 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.311.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.312.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.312.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.312 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.312.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.312 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.312.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.312 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.312.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.312 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.312.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.312 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.312.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.312 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.312.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.312 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.312.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.312 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.312.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.312 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.312.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.312 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.312.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.313.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.313.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.313 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.313.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.313 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.313.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.313 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.313.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.313 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.313.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.313 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.313.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.313 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.313.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.313 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.313.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.313 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.313.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.313 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.313.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.313 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.313.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.314.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.314.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.314 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.314.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.314 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.314.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.314 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.314.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.314 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.314.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.314 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.314.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.314 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.314.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.314 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.314.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.314 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.314.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.314 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.314.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.314 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.314.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.315.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.315.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.315 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.315.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.315 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.315.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.315 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.315.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.315 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.315.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.315 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.315.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.315 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.315.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.315 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.315.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.315 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.315.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.315 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.315.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.315 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.315.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.316.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.316.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.316 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.316.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.316 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.316.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.316 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.316.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.316 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.316.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.316 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.316.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.316 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.316.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.316 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.316.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.316 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.316.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.316 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.316.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.316 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.316.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.317.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.317.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.317 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.317.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.317 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.317.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.317 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.317.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.317 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.317.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.317 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.317.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.317 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.317.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.317 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.317.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.317 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.317.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.317 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.317.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.317 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.317.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.318.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.318.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.318 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.318.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.318 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.318.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.318 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.318.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.318 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.318.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.318 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.318.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.318 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.318.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.318 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.318.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.318 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.318.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.318 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.318.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.318 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.318.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.319.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.319.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.319 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.319.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.319 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.319.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.319 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.319.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.319 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.319.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.319 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.319.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.319 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.319.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.319 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.319.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.319 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.319.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.319 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.319.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.319 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/31/PGA_scaffold34__164_contigs__length_87950420.319.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.320.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.320.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.320 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.320.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.320 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.320.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.320 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.320.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.320 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.320.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.320 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.320.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.320 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.320.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.320 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.320.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.320 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.320.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.320 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.320.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.320 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.320.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.321.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.321.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.321 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.321.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.321 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.321.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.321 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.321.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.321 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.321.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.321 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.321.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.321 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.321.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.321 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.321.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.321 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.321.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.321 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.321.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.321 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.321.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.322.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.322.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.322 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.322.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.322 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.322.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.322 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.322.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.322 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.322.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.322 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.322.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.322 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.322.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.322 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.322.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.322 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.322.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.322 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.322.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.322 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.322.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.323.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.323.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.323 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.323.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.323 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.323.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.323 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.323.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.323 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.323.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.323 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.323.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.323 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.323.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.323 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.323.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.323 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.323.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.323 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.323.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.323 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.323.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.324.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.324.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.324 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.324.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.324 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.324.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.324 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.324.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.324 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.324.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.324 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.324.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.324 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.324.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.324 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.324.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.324 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.324.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.324 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.324.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.324 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.324.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.325.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.325.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.325 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.325.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.325 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.325.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.325 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.325.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.325 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.325.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.325 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.325.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.325 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.325.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.325 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.325.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.325 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.325.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.325 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.325.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.325 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.325.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.326.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.326.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.326 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.326.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.326 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.326.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.326 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.326.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.326 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.326.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.326 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.326.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.326 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.326.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.326 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.326.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.326 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.326.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.326 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.326.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.326 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.326.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.327.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.327.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.327 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.327.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.327 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.327.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.327 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.327.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.327 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.327.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.327 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.327.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.327 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.327.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.327 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.327.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.327 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.327.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.327 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.327.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.327 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.327.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.328.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.328.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.328 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.328.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.328 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.328.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.328 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.328.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.328 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.328.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.328 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.328.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.328 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.328.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.328 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.328.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.328 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.328.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.328 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.328.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.328 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.328.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.329.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.329.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.329 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.329.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.329 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.329.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.329 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.329.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.329 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.329.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.329 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.329.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.329 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.329.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.329 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.329.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.329 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.329.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.329 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.329.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.329 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/32/PGA_scaffold34__164_contigs__length_87950420.329.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.330.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.330.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.330 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.330.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.330 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.330.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.330 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.330.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.330 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.330.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.330 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.330.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.330 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.330.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.330 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.330.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.330 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.330.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.330 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.330.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.330 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.330.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.331.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.331.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.331 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.331.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.331 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.331.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.331 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.331.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.331 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.331.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.331 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.331.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.331 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.331.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.331 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.331.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.331 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.331.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.331 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.331.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.331 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.331.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.332.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.332.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.332 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.332.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:10 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.332 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.332.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.332 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.332.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.332 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.332.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.332 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.332.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:10 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.332 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.332.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.332 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.332.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:10 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.332 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.332.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.332 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.332.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.332 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.332.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:4 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.333.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.333.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.333 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.333.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.333 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.333.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.333 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.333.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.333 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.333.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.333 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.333.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.333 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.333.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.333 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.333.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.333 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.333.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.333 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.333.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.333 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.333.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.334.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.334.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.334 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.334.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.334 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.334.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.334 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.334.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.334 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.334.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.334 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.334.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.334 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.334.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.334 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.334.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.334 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.334.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.334 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.334.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.334 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.334.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.335.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.335.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.335 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.335.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.335 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.335.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.335 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.335.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.335 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.335.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.335 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.335.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.335 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.335.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.335 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.335.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.335 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.335.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.335 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.335.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.335 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.335.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.336.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.336.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.336 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.336.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1851 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.336 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.336.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1802 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.336 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.336.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1822 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.336 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.336.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1789 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.336 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.336.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1800 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.336 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.336.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1837 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.336 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.336.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1809 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.336 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.336.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1841 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.336 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.336.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1788 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.336 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.336.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1811 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.337.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.337.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.337 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.337.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.337 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.337.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.337 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.337.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.337 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.337.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.337 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.337.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.337 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.337.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.337 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.337.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.337 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.337.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.337 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.337.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.337 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.337.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.338.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.338.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.338 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.338.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.338 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.338.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.338 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.338.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.338 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.338.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.338 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.338.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.338 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.338.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.338 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.338.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.338 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.338.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.338 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.338.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.338 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.338.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.339.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.339.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.339 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.339.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.339 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.339.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.339 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.339.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.339 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.339.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.339 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.339.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.339 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.339.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.339 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.339.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.339 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.339.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.339 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.339.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.339 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/33/PGA_scaffold34__164_contigs__length_87950420.339.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.340.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.340.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.340 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.340.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.340 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.340.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.340 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.340.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.340 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.340.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.340 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.340.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.340 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.340.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.340 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.340.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.340 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.340.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.340 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.340.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.340 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.340.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.341.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.341.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.341 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.341.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.341 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.341.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.341 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.341.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.341 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.341.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.341 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.341.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.341 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.341.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.341 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.341.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.341 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.341.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.341 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.341.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.341 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.341.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.342.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.342.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.342 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.342.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.342 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.342.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.342 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.342.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.342 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.342.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.342 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.342.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.342 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.342.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.342 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.342.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.342 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.342.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.342 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.342.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.342 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.342.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.343.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.343.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.343 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.343.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.343 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.343.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:8 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.343 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.343.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.343 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.343.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.343 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.343.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.343 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.343.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.343 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.343.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.343 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.343.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.343 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.343.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.343 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.343.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:2 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.344.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.344.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.344 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.344.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.344 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.344.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.344 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.344.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.344 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.344.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.344 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.344.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.344 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.344.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.344 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.344.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.344 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.344.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.344 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.344.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.344 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.344.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.345.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.345.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.345 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.345.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.345 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.345.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.345 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.345.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.345 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.345.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.345 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.345.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.345 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.345.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.345 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.345.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.345 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.345.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.345 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.345.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.345 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.345.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.346.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.346.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.346 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.346.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:14 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.346 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.346.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.346 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.346.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.346 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.346.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.346 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.346.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.346 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.346.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.346 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.346.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.346 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.346.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.346 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.346.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.346 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.346.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:8 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.347.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.347.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.347 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.347.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.347 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.347.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.347 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.347.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.347 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.347.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.347 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.347.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.347 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.347.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.347 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.347.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.347 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.347.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.347 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.347.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.347 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.347.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.348.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.348.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.348 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.348.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.348 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.348.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.348 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.348.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.348 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.348.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.348 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.348.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.348 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.348.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.348 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.348.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.348 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.348.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.348 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.348.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.348 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.348.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.349.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.349.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.349 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.349.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.349 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.349.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.349 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.349.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.349 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.349.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.349 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.349.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.349 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.349.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.349 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.349.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.349 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.349.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.349 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.349.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.349 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/34/PGA_scaffold34__164_contigs__length_87950420.349.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.350.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.350.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.350 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.350.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.350 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.350.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.350 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.350.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.350 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.350.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.350 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.350.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.350 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.350.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.350 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.350.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.350 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.350.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.350 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.350.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.350 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.350.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.351.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.351.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.351 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.351.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.351 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.351.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.351 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.351.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.351 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.351.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.351 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.351.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.351 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.351.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.351 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.351.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.351 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.351.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.351 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.351.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.351 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.351.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.352.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.352.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.352 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.352.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.352 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.352.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.352 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.352.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.352 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.352.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.352 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.352.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.352 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.352.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.352 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.352.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.352 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.352.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.352 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.352.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.352 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.352.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.353.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.353.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.353 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.353.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.353 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.353.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.353 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.353.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.353 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.353.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.353 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.353.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.353 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.353.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.353 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.353.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.353 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.353.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.353 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.353.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.353 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.353.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.354.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.354.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.354 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.354.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.354 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.354.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.354 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.354.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.354 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.354.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.354 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.354.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.354 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.354.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.354 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.354.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.354 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.354.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.354 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.354.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.354 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.354.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.355.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.355.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.355 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.355.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.355 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.355.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.355 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.355.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.355 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.355.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.355 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.355.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.355 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.355.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.355 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.355.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.355 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.355.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.355 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.355.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.355 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.355.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.356.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.356.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.356 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.356.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.356 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.356.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.356 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.356.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.356 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.356.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.356 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.356.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.356 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.356.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.356 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.356.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.356 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.356.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.356 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.356.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.356 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.356.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.357.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.357.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.357 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.357.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.357 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.357.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.357 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.357.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.357 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.357.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.357 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.357.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.357 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.357.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.357 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.357.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.357 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.357.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.357 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.357.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.357 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.357.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.358.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.358.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.358 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.358.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.358 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.358.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.358 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.358.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.358 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.358.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.358 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.358.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.358 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.358.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.358 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.358.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.358 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.358.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.358 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.358.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.358 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.358.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.359.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.359.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.359 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.359.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.359 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.359.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.359 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.359.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.359 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.359.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.359 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.359.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.359 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.359.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.359 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.359.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.359 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.359.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.359 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.359.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.359 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/35/PGA_scaffold34__164_contigs__length_87950420.359.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.360.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.360.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.360 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.360.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.360 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.360.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.360 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.360.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.360 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.360.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.360 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.360.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.360 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.360.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.360 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.360.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.360 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.360.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.360 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.360.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.360 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.360.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.361.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.361.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.361 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.361.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.361 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.361.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.361 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.361.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.361 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.361.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.361 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.361.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.361 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.361.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.361 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.361.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.361 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.361.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.361 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.361.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.361 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.361.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.362.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.362.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.362 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.362.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.362 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.362.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.362 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.362.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.362 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.362.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.362 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.362.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.362 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.362.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.362 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.362.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.362 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.362.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.362 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.362.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.362 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.362.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.363.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.363.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.363 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.363.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.363 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.363.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.363 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.363.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.363 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.363.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.363 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.363.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.363 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.363.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.363 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.363.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.363 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.363.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.363 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.363.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.363 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.363.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:4 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.364.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.364.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.364 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.364.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.364 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.364.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.364 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.364.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.364 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.364.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.364 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.364.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.364 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.364.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.364 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.364.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.364 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.364.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.364 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.364.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.364 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.364.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.365.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.365.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.365 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.365.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.365 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.365.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.365 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.365.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.365 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.365.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.365 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.365.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.365 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.365.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.365 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.365.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.365 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.365.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.365 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.365.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.365 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.365.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.366.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.366.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.366 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.366.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.366 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.366.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.366 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.366.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.366 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.366.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.366 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.366.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.366 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.366.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.366 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.366.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.366 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.366.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.366 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.366.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.366 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.366.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.367.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.367.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.367 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.367.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.367 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.367.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.367 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.367.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.367 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.367.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.367 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.367.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.367 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.367.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.367 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.367.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.367 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.367.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.367 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.367.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.367 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.367.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.368.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.368.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.368 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.368.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.368 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.368.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.368 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.368.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.368 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.368.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.368 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.368.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.368 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.368.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.368 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.368.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.368 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.368.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.368 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.368.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.368 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.368.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:2 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.369.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.369.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.369 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.369.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.369 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.369.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.369 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.369.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.369 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.369.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.369 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.369.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.369 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.369.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.369 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.369.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.369 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.369.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.369 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.369.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.369 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/36/PGA_scaffold34__164_contigs__length_87950420.369.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.370.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.370.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.370 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.370.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.370 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.370.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.370 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.370.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.370 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.370.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.370 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.370.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.370 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.370.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.370 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.370.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.370 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.370.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.370 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.370.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.370 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.370.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.371.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.371.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.371 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.371.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.371 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.371.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.371 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.371.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.371 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.371.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.371 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.371.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.371 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.371.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.371 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.371.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.371 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.371.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.371 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.371.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.371 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.371.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.372.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.372.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.372 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.372.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.372 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.372.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.372 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.372.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.372 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.372.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.372 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.372.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.372 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.372.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.372 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.372.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.372 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.372.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.372 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.372.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.372 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.372.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.373.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.373.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.373 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.373.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.373 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.373.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.373 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.373.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.373 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.373.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.373 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.373.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.373 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.373.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.373 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.373.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.373 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.373.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.373 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.373.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.373 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.373.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.374.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.374.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.374 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.374.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.374 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.374.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.374 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.374.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.374 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.374.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.374 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.374.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.374 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.374.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.374 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.374.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.374 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.374.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.374 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.374.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.374 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.374.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.375.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.375.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.375 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.375.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.375 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.375.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.375 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.375.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.375 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.375.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.375 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.375.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.375 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.375.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.375 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.375.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.375 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.375.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.375 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.375.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.375 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.375.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.376.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.376.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.376 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.376.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.376 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.376.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.376 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.376.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.376 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.376.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.376 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.376.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.376 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.376.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.376 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.376.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.376 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.376.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.376 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.376.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.376 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.376.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.377.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.377.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.377 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.377.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.377 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.377.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.377 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.377.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.377 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.377.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.377 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.377.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.377 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.377.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.377 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.377.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.377 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.377.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.377 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.377.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.377 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.377.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.378.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.378.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.378 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.378.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.378 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.378.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.378 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.378.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.378 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.378.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.378 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.378.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.378 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.378.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.378 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.378.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.378 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.378.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.378 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.378.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.378 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.378.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.379.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.379.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.379 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.379.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.379 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.379.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.379 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.379.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.379 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.379.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.379 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.379.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.379 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.379.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.379 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.379.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.379 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.379.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.379 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.379.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.379 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/37/PGA_scaffold34__164_contigs__length_87950420.379.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.380.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.380.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.380 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.380.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.380 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.380.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.380 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.380.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.380 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.380.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.380 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.380.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.380 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.380.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.380 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.380.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.380 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.380.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.380 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.380.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.380 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.380.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.381.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.381.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.381 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.381.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.381 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.381.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.381 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.381.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.381 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.381.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.381 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.381.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.381 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.381.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.381 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.381.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.381 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.381.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.381 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.381.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.381 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.381.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.382.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.382.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.382 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.382.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:32 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.382 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.382.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:20 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.382 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.382.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:15 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.382 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.382.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:20 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.382 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.382.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:19 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.382 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.382.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:25 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.382 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.382.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:18 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.382 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.382.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:23 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.382 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.382.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:23 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.382 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.382.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:26 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.383.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.383.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.383 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.383.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.383 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.383.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.383 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.383.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.383 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.383.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.383 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.383.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.383 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.383.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.383 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.383.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.383 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.383.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.383 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.383.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.383 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.383.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.384.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.384.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.384 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.384.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.384 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.384.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.384 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.384.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.384 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.384.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.384 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.384.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.384 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.384.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.384 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.384.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.384 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.384.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.384 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.384.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.384 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.384.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.385.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.385.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.385 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.385.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.385 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.385.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.385 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.385.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.385 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.385.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.385 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.385.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.385 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.385.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.385 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.385.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.385 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.385.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.385 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.385.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.385 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.385.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.386.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.386.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.386 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.386.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.386 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.386.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.386 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.386.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.386 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.386.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.386 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.386.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.386 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.386.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.386 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.386.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.386 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.386.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.386 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.386.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.386 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.386.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.387.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.387.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.387 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.387.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.387 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.387.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.387 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.387.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.387 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.387.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.387 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.387.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.387 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.387.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.387 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.387.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.387 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.387.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.387 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.387.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.387 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.387.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.388.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.388.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.388 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.388.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.388 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.388.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.388 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.388.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.388 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.388.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.388 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.388.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.388 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.388.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.388 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.388.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.388 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.388.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.388 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.388.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.388 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.388.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:5 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.389.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.389.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.389 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.389.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.389 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.389.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.389 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.389.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.389 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.389.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.389 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.389.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.389 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.389.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.389 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.389.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.389 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.389.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.389 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.389.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.389 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/38/PGA_scaffold34__164_contigs__length_87950420.389.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.390.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.390.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.390 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.390.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.390 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.390.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.390 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.390.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.390 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.390.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.390 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.390.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.390 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.390.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.390 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.390.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.390 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.390.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.390 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.390.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.390 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.390.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.391.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.391.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.391 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.391.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.391 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.391.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.391 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.391.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.391 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.391.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.391 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.391.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.391 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.391.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.391 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.391.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.391 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.391.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.391 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.391.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.391 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.391.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.392.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.392.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.392 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.392.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.392 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.392.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.392 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.392.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.392 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.392.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.392 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.392.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.392 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.392.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.392 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.392.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.392 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.392.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.392 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.392.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.392 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.392.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.393.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.393.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.393 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.393.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.393 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.393.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.393 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.393.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.393 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.393.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.393 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.393.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.393 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.393.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.393 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.393.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.393 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.393.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.393 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.393.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.393 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.393.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.394.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.394.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.394 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.394.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.394 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.394.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.394 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.394.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.394 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.394.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.394 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.394.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.394 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.394.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.394 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.394.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.394 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.394.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.394 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.394.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.394 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.394.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:4 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.395.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.395.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.395 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.395.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.395 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.395.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.395 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.395.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.395 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.395.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.395 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.395.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.395 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.395.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.395 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.395.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.395 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.395.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.395 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.395.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.395 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.395.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.396.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.396.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.396 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.396.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.396 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.396.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.396 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.396.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.396 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.396.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.396 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.396.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.396 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.396.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.396 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.396.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.396 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.396.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.396 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.396.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.396 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.396.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.397.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.397.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.397 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.397.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.397 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.397.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.397 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.397.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.397 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.397.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.397 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.397.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.397 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.397.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.397 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.397.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.397 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.397.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.397 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.397.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.397 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.397.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.398.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.398.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.398 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.398.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.398 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.398.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.398 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.398.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.398 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.398.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.398 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.398.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.398 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.398.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.398 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.398.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.398 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.398.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.398 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.398.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.398 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.398.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.399.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.399.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.399 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.399.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.399 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.399.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.399 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.399.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.399 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.399.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.399 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.399.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.399 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.399.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.399 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.399.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.399 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.399.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.399 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.399.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.399 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/39/PGA_scaffold34__164_contigs__length_87950420.399.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.400.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.400.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.400 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.400.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.400 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.400.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.400 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.400.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.400 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.400.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.400 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.400.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.400 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.400.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.400 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.400.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.400 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.400.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.400 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.400.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.400 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.400.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.401.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.401.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.401 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.401.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.401 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.401.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.401 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.401.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.401 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.401.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.401 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.401.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.401 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.401.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.401 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.401.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.401 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.401.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.401 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.401.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.401 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.401.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.402.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.402.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.402 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.402.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.402 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.402.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.402 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.402.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.402 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.402.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.402 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.402.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.402 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.402.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.402 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.402.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.402 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.402.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.402 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.402.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.402 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.402.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.403.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.403.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.403 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.403.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.403 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.403.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.403 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.403.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.403 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.403.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.403 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.403.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.403 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.403.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.403 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.403.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.403 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.403.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.403 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.403.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.403 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.403.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.404.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.404.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.404 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.404.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.404 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.404.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.404 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.404.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.404 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.404.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.404 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.404.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.404 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.404.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.404 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.404.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.404 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.404.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.404 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.404.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.404 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.404.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.405.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.405.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.405 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.405.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.405 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.405.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.405 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.405.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.405 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.405.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.405 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.405.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.405 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.405.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.405 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.405.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.405 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.405.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.405 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.405.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.405 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.405.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.406.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.406.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.406 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.406.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.406 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.406.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.406 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.406.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.406 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.406.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.406 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.406.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.406 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.406.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.406 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.406.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.406 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.406.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.406 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.406.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.406 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.406.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.407.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.407.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.407 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.407.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.407 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.407.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.407 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.407.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.407 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.407.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.407 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.407.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.407 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.407.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.407 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.407.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.407 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.407.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.407 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.407.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.407 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.407.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.408.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.408.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.408 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.408.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.408 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.408.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.408 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.408.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.408 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.408.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.408 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.408.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.408 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.408.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.408 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.408.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.408 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.408.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.408 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.408.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.408 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.408.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.409.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.409.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.409 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.409.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.409 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.409.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.409 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.409.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.409 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.409.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.409 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.409.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.409 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.409.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.409 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.409.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.409 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.409.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.409 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.409.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.409 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/40/PGA_scaffold34__164_contigs__length_87950420.409.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.410.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.410.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.410 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.410.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.410 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.410.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.410 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.410.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.410 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.410.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.410 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.410.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.410 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.410.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.410 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.410.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.410 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.410.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.410 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.410.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.410 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.410.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.411.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.411.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.411 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.411.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.411 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.411.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.411 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.411.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.411 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.411.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.411 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.411.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.411 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.411.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.411 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.411.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.411 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.411.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.411 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.411.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.411 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.411.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.412.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.412.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.412 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.412.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:71 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.412 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.412.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:47 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.412 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.412.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:36 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.412 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.412.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:43 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.412 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.412.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:49 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.412 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.412.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:60 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.412 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.412.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:43 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.412 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.412.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:52 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.412 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.412.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:59 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.412 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.412.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:44 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.413.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.413.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.413 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.413.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.413 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.413.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.413 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.413.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.413 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.413.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.413 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.413.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.413 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.413.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.413 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.413.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.413 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.413.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.413 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.413.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.413 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.413.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.414.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.414.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.414 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.414.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:14 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.414 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.414.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:10 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.414 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.414.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.414 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.414.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.414 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.414.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:10 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.414 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.414.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.414 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.414.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.414 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.414.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.414 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.414.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.414 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.414.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:6 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.415.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.415.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.415 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.415.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:42 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.415 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.415.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:28 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.415 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.415.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:17 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.415 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.415.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:28 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.415 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.415.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:27 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.415 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.415.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:39 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.415 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.415.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:25 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.415 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.415.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:41 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.415 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.415.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:34 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.415 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.415.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:34 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.416.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.416.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.416 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.416.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.416 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.416.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.416 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.416.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.416 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.416.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.416 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.416.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.416 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.416.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.416 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.416.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.416 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.416.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.416 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.416.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.416 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.416.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.417.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.417.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.417 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.417.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.417 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.417.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.417 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.417.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.417 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.417.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.417 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.417.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.417 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.417.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.417 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.417.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.417 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.417.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.417 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.417.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.417 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.417.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.418.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.418.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.418 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.418.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.418 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.418.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.418 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.418.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.418 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.418.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.418 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.418.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.418 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.418.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.418 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.418.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.418 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.418.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.418 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.418.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.418 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.418.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.419.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.419.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.419 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.419.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.419 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.419.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.419 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.419.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.419 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.419.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.419 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.419.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.419 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.419.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.419 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.419.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.419 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.419.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.419 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.419.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.419 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/41/PGA_scaffold34__164_contigs__length_87950420.419.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.420.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.420.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.420 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.420.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.420 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.420.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.420 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.420.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.420 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.420.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.420 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.420.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.420 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.420.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.420 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.420.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.420 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.420.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.420 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.420.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.420 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.420.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.421.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.421.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.421 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.421.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.421 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.421.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.421 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.421.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.421 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.421.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.421 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.421.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.421 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.421.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.421 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.421.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.421 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.421.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.421 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.421.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.421 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.421.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.422.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.422.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.422 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.422.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.422 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.422.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.422 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.422.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.422 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.422.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.422 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.422.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.422 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.422.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.422 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.422.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.422 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.422.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.422 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.422.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.422 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.422.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.423.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.423.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.423 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.423.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.423 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.423.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.423 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.423.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.423 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.423.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.423 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.423.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.423 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.423.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.423 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.423.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.423 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.423.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.423 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.423.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.423 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.423.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:4 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.424.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.424.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.424 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.424.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.424 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.424.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.424 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.424.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.424 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.424.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.424 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.424.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.424 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.424.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.424 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.424.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.424 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.424.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.424 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.424.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.424 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.424.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:2 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.425.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.425.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.425 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.425.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.425 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.425.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.425 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.425.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.425 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.425.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.425 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.425.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.425 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.425.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.425 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.425.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.425 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.425.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.425 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.425.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.425 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.425.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:2 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.426.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.426.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.426 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.426.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.426 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.426.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.426 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.426.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.426 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.426.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.426 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.426.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.426 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.426.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.426 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.426.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.426 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.426.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.426 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.426.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.426 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.426.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.427.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.427.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.427 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.427.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.427 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.427.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.427 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.427.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.427 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.427.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.427 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.427.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.427 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.427.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.427 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.427.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.427 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.427.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.427 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.427.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.427 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.427.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.428.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.428.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.428 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.428.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.428 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.428.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.428 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.428.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.428 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.428.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.428 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.428.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.428 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.428.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.428 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.428.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.428 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.428.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.428 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.428.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.428 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.428.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.429.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.429.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.429 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.429.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.429 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.429.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.429 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.429.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.429 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.429.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.429 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.429.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.429 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.429.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.429 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.429.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.429 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.429.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.429 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.429.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.429 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/42/PGA_scaffold34__164_contigs__length_87950420.429.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.430.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.430.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.430 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.430.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.430 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.430.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.430 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.430.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.430 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.430.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.430 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.430.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.430 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.430.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.430 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.430.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.430 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.430.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.430 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.430.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.430 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.430.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.431.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.431.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.431 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.431.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.431 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.431.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.431 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.431.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.431 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.431.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.431 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.431.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.431 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.431.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.431 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.431.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.431 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.431.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.431 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.431.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.431 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.431.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.432.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.432.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.432 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.432.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.432 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.432.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.432 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.432.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.432 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.432.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.432 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.432.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.432 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.432.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.432 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.432.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.432 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.432.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.432 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.432.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.432 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.432.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.433.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.433.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.433 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.433.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.433 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.433.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.433 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.433.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.433 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.433.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.433 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.433.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.433 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.433.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.433 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.433.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.433 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.433.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.433 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.433.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.433 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.433.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.434.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.434.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.434 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.434.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.434 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.434.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.434 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.434.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.434 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.434.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.434 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.434.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.434 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.434.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.434 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.434.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.434 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.434.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.434 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.434.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.434 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.434.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.435.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.435.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.435 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.435.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.435 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.435.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.435 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.435.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.435 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.435.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.435 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.435.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.435 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.435.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.435 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.435.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.435 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.435.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.435 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.435.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.435 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.435.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.436.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.436.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.436 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.436.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.436 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.436.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.436 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.436.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.436 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.436.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.436 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.436.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.436 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.436.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.436 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.436.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.436 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.436.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.436 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.436.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.436 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.436.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.437.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.437.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.437 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.437.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:12 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.437 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.437.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.437 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.437.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.437 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.437.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.437 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.437.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:10 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.437 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.437.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.437 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.437.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.437 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.437.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.437 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.437.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.437 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.437.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:5 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.438.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.438.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.438 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.438.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:17 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.438 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.438.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:17 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.438 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.438.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.438 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.438.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:10 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.438 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.438.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:11 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.438 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.438.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:11 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.438 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.438.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:10 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.438 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.438.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.438 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.438.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:10 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.438 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.438.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:16 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.439.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.439.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.439 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.439.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.439 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.439.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.439 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.439.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.439 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.439.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.439 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.439.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.439 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.439.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.439 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.439.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.439 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.439.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.439 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.439.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.439 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/43/PGA_scaffold34__164_contigs__length_87950420.439.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.440.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.440.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.440 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.440.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.440 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.440.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.440 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.440.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.440 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.440.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.440 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.440.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.440 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.440.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.440 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.440.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.440 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.440.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.440 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.440.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.440 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.440.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.441.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.441.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.441 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.441.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.441 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.441.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.441 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.441.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.441 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.441.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.441 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.441.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.441 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.441.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.441 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.441.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.441 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.441.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.441 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.441.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.441 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.441.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.442.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.442.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.442 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.442.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.442 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.442.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.442 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.442.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.442 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.442.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.442 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.442.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.442 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.442.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.442 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.442.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.442 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.442.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.442 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.442.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.442 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.442.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.443.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.443.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.443 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.443.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.443 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.443.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.443 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.443.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.443 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.443.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.443 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.443.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.443 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.443.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.443 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.443.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.443 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.443.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.443 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.443.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.443 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.443.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.444.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.444.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.444 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.444.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.444 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.444.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.444 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.444.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.444 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.444.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.444 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.444.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.444 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.444.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.444 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.444.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.444 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.444.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.444 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.444.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.444 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.444.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.445.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.445.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.445 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.445.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:61 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.445 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.445.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:42 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.445 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.445.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:33 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.445 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.445.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:37 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.445 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.445.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:40 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.445 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.445.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:47 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.445 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.445.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:34 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.445 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.445.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:49 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.445 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.445.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:50 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.445 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.445.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:36 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.446.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.446.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.446 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.446.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.446 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.446.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.446 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.446.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.446 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.446.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.446 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.446.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.446 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.446.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.446 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.446.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.446 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.446.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.446 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.446.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.446 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.446.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.447.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.447.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.447 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.447.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.447 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.447.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.447 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.447.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.447 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.447.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.447 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.447.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.447 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.447.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.447 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.447.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.447 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.447.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.447 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.447.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.447 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.447.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.448.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.448.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.448 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.448.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.448 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.448.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.448 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.448.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.448 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.448.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.448 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.448.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.448 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.448.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.448 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.448.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.448 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.448.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.448 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.448.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.448 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.448.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:4 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.449.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.449.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.449 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.449.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.449 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.449.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.449 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.449.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.449 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.449.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.449 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.449.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.449 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.449.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.449 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.449.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.449 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.449.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.449 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.449.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.449 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/44/PGA_scaffold34__164_contigs__length_87950420.449.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.450.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.450.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.450 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.450.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.450 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.450.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.450 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.450.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.450 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.450.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.450 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.450.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.450 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.450.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.450 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.450.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.450 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.450.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.450 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.450.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.450 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.450.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.451.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.451.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.451 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.451.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.451 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.451.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.451 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.451.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.451 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.451.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.451 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.451.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.451 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.451.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.451 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.451.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.451 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.451.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.451 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.451.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.451 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.451.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.452.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.452.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.452 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.452.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.452 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.452.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.452 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.452.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.452 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.452.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.452 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.452.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.452 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.452.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.452 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.452.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.452 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.452.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.452 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.452.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.452 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.452.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.453.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.453.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.453 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.453.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.453 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.453.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.453 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.453.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.453 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.453.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.453 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.453.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.453 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.453.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.453 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.453.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.453 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.453.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.453 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.453.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.453 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.453.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.454.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.454.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.454 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.454.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.454 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.454.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.454 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.454.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.454 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.454.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.454 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.454.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.454 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.454.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.454 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.454.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.454 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.454.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.454 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.454.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.454 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.454.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.455.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.455.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.455 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.455.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.455 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.455.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.455 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.455.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.455 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.455.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.455 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.455.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.455 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.455.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.455 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.455.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.455 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.455.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.455 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.455.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.455 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.455.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.456.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.456.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.456 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.456.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:82 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.456 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.456.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:49 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.456 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.456.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:54 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.456 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.456.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:64 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.456 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.456.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:63 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.456 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.456.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:75 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.456 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.456.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:55 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.456 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.456.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:64 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.456 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.456.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:70 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.456 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.456.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:58 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.457.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.457.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.457 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.457.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.457 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.457.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.457 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.457.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.457 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.457.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.457 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.457.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.457 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.457.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.457 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.457.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.457 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.457.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.457 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.457.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.457 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.457.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.458.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.458.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.458 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.458.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.458 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.458.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.458 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.458.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.458 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.458.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.458 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.458.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.458 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.458.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.458 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.458.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.458 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.458.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.458 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.458.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.458 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.458.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.459.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.459.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.459 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.459.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.459 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.459.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.459 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.459.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.459 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.459.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.459 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.459.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.459 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.459.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.459 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.459.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.459 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.459.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.459 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.459.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.459 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/45/PGA_scaffold34__164_contigs__length_87950420.459.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.460.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.460.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.460 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.460.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.460 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.460.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.460 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.460.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.460 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.460.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.460 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.460.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.460 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.460.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.460 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.460.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.460 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.460.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.460 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.460.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.460 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.460.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.461.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.461.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.461 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.461.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:85 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.461 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.461.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:44 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.461 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.461.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:41 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.461 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.461.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:54 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.461 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.461.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:59 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.461 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.461.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:70 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.461 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.461.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:49 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.461 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.461.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:58 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.461 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.461.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:57 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.461 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.461.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:55 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.462.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.462.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.462 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.462.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.462 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.462.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.462 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.462.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.462 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.462.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.462 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.462.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.462 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.462.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.462 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.462.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.462 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.462.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.462 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.462.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.462 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.462.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.463.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.463.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.463 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.463.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.463 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.463.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.463 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.463.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.463 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.463.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.463 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.463.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.463 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.463.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.463 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.463.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.463 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.463.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.463 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.463.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.463 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.463.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.464.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.464.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.464 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.464.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.464 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.464.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.464 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.464.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.464 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.464.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.464 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.464.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.464 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.464.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.464 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.464.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.464 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.464.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.464 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.464.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.464 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.464.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.465.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.465.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.465 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.465.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.465 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.465.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.465 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.465.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.465 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.465.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.465 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.465.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.465 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.465.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.465 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.465.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.465 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.465.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.465 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.465.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.465 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.465.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.466.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.466.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.466 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.466.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.466 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.466.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.466 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.466.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.466 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.466.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.466 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.466.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.466 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.466.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.466 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.466.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.466 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.466.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.466 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.466.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.466 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.466.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.467.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.467.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.467 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.467.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.467 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.467.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.467 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.467.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.467 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.467.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.467 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.467.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.467 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.467.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.467 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.467.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.467 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.467.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.467 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.467.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.467 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.467.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.468.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.468.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.468 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.468.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1754 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.468 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.468.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1706 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.468 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.468.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1722 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.468 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.468.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1704 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.468 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.468.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1696 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.468 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.468.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1739 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.468 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.468.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1730 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.468 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.468.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1750 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.468 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.468.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1698 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.468 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.468.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1705 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.469.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.469.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.469 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.469.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.469 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.469.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.469 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.469.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.469 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.469.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.469 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.469.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.469 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.469.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.469 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.469.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.469 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.469.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.469 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.469.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.469 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/46/PGA_scaffold34__164_contigs__length_87950420.469.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.470.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.470.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.470 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.470.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.470 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.470.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.470 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.470.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.470 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.470.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.470 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.470.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.470 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.470.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.470 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.470.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.470 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.470.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.470 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.470.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.470 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.470.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.471.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.471.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.471 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.471.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.471 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.471.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.471 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.471.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.471 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.471.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.471 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.471.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.471 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.471.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.471 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.471.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.471 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.471.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.471 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.471.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.471 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.471.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.472.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.472.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.472 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.472.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.472 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.472.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.472 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.472.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.472 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.472.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.472 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.472.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.472 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.472.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.472 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.472.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.472 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.472.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.472 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.472.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.472 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.472.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.473.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.473.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.473 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.473.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.473 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.473.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.473 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.473.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.473 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.473.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.473 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.473.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.473 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.473.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.473 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.473.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.473 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.473.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.473 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.473.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.473 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.473.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.474.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.474.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.474 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.474.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.474 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.474.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.474 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.474.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.474 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.474.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.474 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.474.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.474 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.474.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.474 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.474.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:-1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.474 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.474.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.474 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.474.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.474 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.474.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.475.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.475.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.475 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.475.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.475 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.475.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.475 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.475.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.475 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.475.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.475 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.475.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.475 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.475.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.475 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.475.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.475 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.475.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.475 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.475.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.475 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.475.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:2 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.476.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.476.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.476 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.476.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.476 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.476.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.476 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.476.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.476 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.476.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.476 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.476.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.476 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.476.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.476 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.476.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.476 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.476.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.476 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.476.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.476 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.476.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.477.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.477.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.477 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.477.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.477 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.477.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.477 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.477.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.477 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.477.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.477 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.477.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.477 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.477.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.477 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.477.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.477 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.477.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.477 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.477.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.477 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.477.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.478.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.478.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.478 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.478.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.478 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.478.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.478 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.478.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.478 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.478.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.478 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.478.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.478 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.478.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.478 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.478.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.478 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.478.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.478 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.478.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.478 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.478.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.479.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.479.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.479 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.479.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.479 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.479.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.479 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.479.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.479 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.479.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.479 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.479.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.479 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.479.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.479 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.479.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.479 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.479.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.479 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.479.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.479 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/47/PGA_scaffold34__164_contigs__length_87950420.479.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.480.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.480.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.480 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.480.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.480 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.480.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.480 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.480.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.480 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.480.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.480 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.480.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.480 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.480.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.480 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.480.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.480 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.480.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.480 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.480.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.480 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.480.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.481.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.481.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.481 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.481.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.481 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.481.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.481 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.481.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.481 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.481.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.481 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.481.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.481 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.481.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.481 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.481.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.481 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.481.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.481 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.481.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.481 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.481.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.482.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.482.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.482 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.482.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.482 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.482.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.482 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.482.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.482 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.482.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.482 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.482.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.482 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.482.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.482 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.482.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.482 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.482.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.482 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.482.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.482 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.482.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.483.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.483.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.483 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.483.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.483 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.483.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.483 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.483.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.483 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.483.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.483 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.483.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.483 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.483.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.483 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.483.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.483 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.483.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.483 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.483.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.483 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.483.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.484.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.484.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.484 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.484.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.484 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.484.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.484 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.484.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.484 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.484.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.484 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.484.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.484 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.484.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.484 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.484.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.484 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.484.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.484 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.484.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.484 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.484.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.485.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.485.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.485 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.485.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.485 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.485.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.485 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.485.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.485 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.485.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.485 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.485.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.485 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.485.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.485 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.485.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.485 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.485.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.485 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.485.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.485 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.485.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.486.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.486.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.486 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.486.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.486 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.486.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.486 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.486.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.486 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.486.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.486 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.486.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.486 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.486.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.486 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.486.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.486 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.486.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.486 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.486.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.486 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.486.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.487.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.487.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.487 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.487.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:15 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.487 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.487.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:8 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.487 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.487.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.487 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.487.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:8 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.487 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.487.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:10 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.487 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.487.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:8 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.487 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.487.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.487 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.487.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.487 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.487.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:8 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.487 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.487.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:9 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.488.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.488.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.488 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.488.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:17 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.488 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.488.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:13 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.488 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.488.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.488 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.488.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.488 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.488.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:12 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.488 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.488.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.488 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.488.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:8 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.488 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.488.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.488 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.488.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.488 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.488.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:9 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.489.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.489.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.489 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.489.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.489 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.489.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.489 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.489.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.489 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.489.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.489 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.489.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.489 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.489.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.489 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.489.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.489 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.489.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.489 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.489.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.489 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/48/PGA_scaffold34__164_contigs__length_87950420.489.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.490.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.490.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.490 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.490.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.490 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.490.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.490 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.490.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.490 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.490.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.490 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.490.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.490 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.490.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.490 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.490.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.490 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.490.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.490 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.490.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.490 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.490.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.491.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.491.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.491 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.491.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.491 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.491.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.491 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.491.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.491 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.491.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.491 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.491.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.491 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.491.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.491 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.491.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.491 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.491.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.491 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.491.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.491 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.491.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.492.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.492.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.492 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.492.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.492 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.492.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.492 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.492.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.492 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.492.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.492 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.492.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.492 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.492.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.492 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.492.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.492 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.492.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.492 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.492.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.492 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.492.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.493.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.493.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.493 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.493.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.493 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.493.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.493 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.493.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.493 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.493.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.493 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.493.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.493 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.493.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.493 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.493.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.493 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.493.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.493 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.493.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.493 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.493.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.494.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.494.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.494 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.494.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.494 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.494.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.494 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.494.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.494 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.494.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.494 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.494.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.494 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.494.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.494 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.494.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.494 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.494.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.494 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.494.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.494 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.494.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.495.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.495.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.495 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.495.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.495 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.495.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.495 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.495.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.495 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.495.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.495 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.495.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.495 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.495.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.495 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.495.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.495 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.495.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.495 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.495.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.495 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.495.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.496.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.496.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.496 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.496.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.496 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.496.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.496 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.496.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.496 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.496.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.496 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.496.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.496 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.496.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.496 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.496.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.496 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.496.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.496 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.496.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.496 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.496.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.497.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.497.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.497 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.497.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.497 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.497.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.497 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.497.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.497 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.497.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.497 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.497.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.497 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.497.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.497 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.497.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.497 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.497.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.497 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.497.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.497 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.497.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.498.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.498.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.498 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.498.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.498 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.498.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.498 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.498.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.498 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.498.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.498 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.498.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.498 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.498.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.498 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.498.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.498 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.498.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.498 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.498.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.498 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.498.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.499.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.499.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.499 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.499.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.499 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.499.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.499 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.499.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.499 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.499.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.499 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.499.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.499 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.499.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.499 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.499.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.499 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.499.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.499 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.499.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.499 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/49/PGA_scaffold34__164_contigs__length_87950420.499.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.500.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.500.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.500 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.500.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.500 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.500.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.500 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.500.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.500 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.500.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.500 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.500.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.500 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.500.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.500 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.500.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.500 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.500.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.500 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.500.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.500 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.500.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.501.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.501.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.501 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.501.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.501 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.501.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.501 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.501.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.501 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.501.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.501 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.501.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.501 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.501.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.501 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.501.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.501 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.501.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.501 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.501.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.501 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.501.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.502.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.502.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.502 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.502.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.502 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.502.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.502 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.502.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.502 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.502.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.502 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.502.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.502 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.502.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.502 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.502.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.502 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.502.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.502 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.502.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.502 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.502.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.503.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.503.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.503 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.503.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.503 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.503.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.503 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.503.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.503 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.503.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.503 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.503.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.503 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.503.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.503 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.503.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.503 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.503.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.503 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.503.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.503 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.503.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.504.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.504.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.504 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.504.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.504 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.504.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.504 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.504.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.504 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.504.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.504 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.504.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.504 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.504.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.504 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.504.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.504 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.504.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.504 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.504.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.504 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.504.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.505.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.505.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.505 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.505.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.505 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.505.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.505 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.505.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.505 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.505.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.505 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.505.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.505 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.505.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.505 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.505.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.505 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.505.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.505 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.505.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.505 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.505.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.506.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.506.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.506 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.506.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.506 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.506.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.506 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.506.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.506 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.506.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.506 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.506.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.506 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.506.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.506 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.506.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.506 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.506.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.506 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.506.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.506 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.506.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.507.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.507.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.507 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.507.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.507 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.507.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.507 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.507.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.507 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.507.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.507 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.507.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.507 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.507.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.507 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.507.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.507 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.507.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.507 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.507.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.507 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.507.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.508.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.508.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.508 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.508.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.508 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.508.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.508 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.508.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.508 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.508.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.508 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.508.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.508 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.508.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.508 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.508.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.508 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.508.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.508 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.508.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.508 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.508.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.509.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.509.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.509 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.509.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.509 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.509.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.509 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.509.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.509 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.509.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.509 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.509.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.509 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.509.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.509 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.509.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.509 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.509.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.509 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.509.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.509 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/50/PGA_scaffold34__164_contigs__length_87950420.509.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.510.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.510.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.510 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.510.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.510 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.510.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.510 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.510.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.510 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.510.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.510 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.510.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.510 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.510.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.510 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.510.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.510 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.510.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.510 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.510.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.510 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.510.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.511.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.511.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.511 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.511.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.511 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.511.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.511 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.511.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.511 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.511.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.511 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.511.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.511 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.511.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.511 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.511.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.511 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.511.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.511 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.511.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.511 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.511.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.512.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.512.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.512 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.512.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.512 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.512.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.512 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.512.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.512 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.512.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.512 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.512.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.512 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.512.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.512 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.512.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.512 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.512.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.512 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.512.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.512 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.512.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.513.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.513.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.513 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.513.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.513 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.513.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.513 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.513.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.513 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.513.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.513 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.513.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.513 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.513.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.513 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.513.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.513 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.513.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.513 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.513.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.513 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.513.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.514.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.514.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.514 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.514.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.514 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.514.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.514 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.514.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.514 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.514.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.514 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.514.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.514 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.514.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.514 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.514.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.514 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.514.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.514 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.514.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.514 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.514.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.515.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.515.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.515 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.515.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.515 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.515.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.515 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.515.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.515 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.515.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.515 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.515.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.515 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.515.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.515 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.515.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.515 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.515.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.515 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.515.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.515 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.515.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.516.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.516.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.516 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.516.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.516 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.516.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.516 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.516.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.516 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.516.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.516 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.516.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.516 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.516.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.516 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.516.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.516 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.516.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.516 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.516.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.516 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.516.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.517.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.517.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.517 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.517.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.517 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.517.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.517 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.517.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.517 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.517.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.517 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.517.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.517 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.517.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.517 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.517.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.517 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.517.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.517 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.517.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.517 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.517.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.518.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.518.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.518 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.518.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.518 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.518.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.518 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.518.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.518 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.518.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.518 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.518.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.518 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.518.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.518 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.518.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.518 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.518.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.518 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.518.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.518 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.518.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.519.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.519.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.519 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.519.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:73 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.519 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.519.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:55 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.519 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.519.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:44 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.519 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.519.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:51 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.519 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.519.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:59 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.519 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.519.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:68 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.519 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.519.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:49 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.519 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.519.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:57 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.519 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.519.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:64 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.519 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/51/PGA_scaffold34__164_contigs__length_87950420.519.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:53 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.520.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.520.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.520 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.520.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.520 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.520.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.520 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.520.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.520 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.520.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.520 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.520.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.520 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.520.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.520 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.520.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.520 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.520.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.520 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.520.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.520 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.520.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.521.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.521.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.521 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.521.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.521 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.521.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.521 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.521.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.521 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.521.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.521 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.521.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.521 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.521.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.521 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.521.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.521 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.521.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.521 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.521.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.521 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.521.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.522.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.522.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.522 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.522.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.522 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.522.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.522 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.522.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.522 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.522.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.522 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.522.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.522 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.522.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.522 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.522.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.522 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.522.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.522 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.522.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.522 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.522.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:2 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.523.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.523.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.523 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.523.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.523 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.523.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.523 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.523.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.523 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.523.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.523 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.523.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.523 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.523.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.523 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.523.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.523 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.523.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.523 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.523.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.523 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.523.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.524.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.524.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.524 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.524.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.524 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.524.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.524 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.524.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.524 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.524.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.524 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.524.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.524 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.524.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.524 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.524.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.524 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.524.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.524 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.524.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.524 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.524.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.525.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.525.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.525 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.525.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.525 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.525.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.525 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.525.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.525 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.525.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.525 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.525.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.525 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.525.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.525 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.525.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.525 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.525.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.525 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.525.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.525 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.525.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.526.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.526.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.526 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.526.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.526 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.526.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.526 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.526.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.526 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.526.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.526 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.526.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.526 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.526.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.526 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.526.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.526 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.526.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.526 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.526.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.526 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.526.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:2 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.527.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.527.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.527 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.527.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.527 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.527.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.527 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.527.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.527 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.527.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.527 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.527.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.527 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.527.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.527 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.527.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.527 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.527.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.527 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.527.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.527 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.527.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.528.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.528.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.528 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.528.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.528 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.528.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.528 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.528.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.528 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.528.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.528 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.528.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.528 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.528.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.528 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.528.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.528 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.528.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.528 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.528.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.528 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.528.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.529.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.529.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.529 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.529.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.529 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.529.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.529 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.529.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.529 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.529.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.529 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.529.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.529 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.529.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.529 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.529.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.529 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.529.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.529 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.529.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.529 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/52/PGA_scaffold34__164_contigs__length_87950420.529.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.530.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.530.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.530 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.530.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.530 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.530.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.530 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.530.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.530 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.530.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.530 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.530.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.530 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.530.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.530 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.530.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.530 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.530.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.530 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.530.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.530 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.530.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.531.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.531.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.531 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.531.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.531 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.531.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.531 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.531.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.531 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.531.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.531 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.531.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.531 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.531.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.531 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.531.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.531 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.531.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.531 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.531.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.531 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.531.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.532.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.532.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.532 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.532.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.532 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.532.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.532 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.532.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.532 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.532.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.532 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.532.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.532 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.532.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.532 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.532.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.532 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.532.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.532 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.532.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.532 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.532.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.533.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.533.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.533 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.533.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.533 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.533.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.533 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.533.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.533 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.533.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.533 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.533.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.533 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.533.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.533 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.533.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.533 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.533.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.533 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.533.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.533 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.533.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.534.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.534.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.534 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.534.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.534 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.534.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.534 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.534.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.534 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.534.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.534 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.534.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.534 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.534.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.534 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.534.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.534 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.534.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.534 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.534.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.534 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.534.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.535.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.535.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.535 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.535.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.535 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.535.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.535 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.535.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.535 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.535.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.535 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.535.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.535 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.535.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.535 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.535.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.535 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.535.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.535 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.535.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.535 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.535.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.536.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.536.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.536 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.536.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.536 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.536.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.536 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.536.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.536 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.536.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.536 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.536.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.536 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.536.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.536 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.536.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.536 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.536.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.536 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.536.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.536 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.536.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.537.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.537.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.537 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.537.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.537 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.537.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.537 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.537.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.537 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.537.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.537 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.537.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.537 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.537.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.537 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.537.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.537 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.537.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.537 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.537.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.537 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.537.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.538.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.538.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.538 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.538.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:34 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.538 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.538.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:29 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.538 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.538.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:19 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.538 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.538.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:24 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.538 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.538.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:20 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.538 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.538.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:33 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.538 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.538.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:15 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.538 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.538.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:32 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.538 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.538.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:35 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.538 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.538.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:25 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.539.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.539.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.539 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.539.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:36 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.539 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.539.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:32 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.539 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.539.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:16 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.539 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.539.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:28 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.539 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.539.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:26 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.539 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.539.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:32 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.539 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.539.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:25 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.539 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.539.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:29 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.539 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.539.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:23 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.539 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/53/PGA_scaffold34__164_contigs__length_87950420.539.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:24 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.540.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.540.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.540 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.540.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:68 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.540 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.540.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:41 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.540 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.540.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:46 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.540 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.540.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:49 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.540 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.540.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:46 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.540 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.540.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:65 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.540 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.540.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:43 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.540 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.540.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:49 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.540 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.540.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:45 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.540 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.540.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:45 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.541.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.541.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.541 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.541.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.541 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.541.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.541 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.541.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.541 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.541.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.541 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.541.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.541 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.541.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.541 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.541.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.541 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.541.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.541 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.541.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.541 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.541.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.542.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.542.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.542 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.542.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.542 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.542.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.542 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.542.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.542 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.542.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.542 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.542.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.542 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.542.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.542 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.542.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.542 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.542.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.542 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.542.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.542 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.542.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.543.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.543.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.543 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.543.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:41 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.543 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.543.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:32 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.543 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.543.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:25 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.543 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.543.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:28 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.543 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.543.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:32 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.543 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.543.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:44 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.543 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.543.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:28 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.543 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.543.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:37 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.543 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.543.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:33 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.543 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.543.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:33 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.544.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.544.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.544 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.544.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.544 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.544.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.544 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.544.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.544 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.544.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.544 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.544.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.544 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.544.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.544 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.544.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.544 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.544.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.544 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.544.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.544 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.544.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.545.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.545.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.545 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.545.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.545 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.545.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.545 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.545.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.545 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.545.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.545 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.545.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.545 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.545.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.545 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.545.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.545 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.545.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.545 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.545.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.545 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.545.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.546.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.546.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.546 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.546.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.546 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.546.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.546 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.546.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.546 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.546.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.546 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.546.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.546 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.546.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.546 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.546.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.546 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.546.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.546 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.546.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.546 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.546.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.547.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.547.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.547 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.547.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.547 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.547.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.547 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.547.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.547 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.547.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.547 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.547.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.547 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.547.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.547 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.547.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.547 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.547.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.547 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.547.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.547 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.547.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.548.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.548.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.548 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.548.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.548 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.548.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.548 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.548.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.548 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.548.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.548 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.548.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.548 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.548.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.548 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.548.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.548 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.548.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.548 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.548.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.548 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.548.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.549.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.549.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.549 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.549.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.549 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.549.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.549 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.549.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.549 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.549.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.549 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.549.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.549 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.549.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.549 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.549.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.549 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.549.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.549 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.549.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.549 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/54/PGA_scaffold34__164_contigs__length_87950420.549.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.550.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.550.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.550 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.550.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.550 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.550.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.550 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.550.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.550 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.550.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.550 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.550.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.550 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.550.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.550 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.550.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.550 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.550.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.550 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.550.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.550 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.550.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.551.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.551.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.551 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.551.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:28 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.551 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.551.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:10 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.551 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.551.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.551 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.551.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.551 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.551.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:20 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.551 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.551.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:16 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.551 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.551.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:14 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.551 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.551.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:12 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.551 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.551.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:15 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.551 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.551.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:14 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.552.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.552.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.552 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.552.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.552 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.552.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.552 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.552.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.552 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.552.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.552 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.552.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.552 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.552.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.552 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.552.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.552 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.552.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.552 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.552.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.552 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.552.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.553.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.553.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.553 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.553.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.553 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.553.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.553 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.553.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.553 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.553.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:10 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.553 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.553.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.553 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.553.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.553 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.553.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:10 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.553 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.553.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.553 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.553.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.553 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.553.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:8 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.554.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.554.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.554 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.554.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.554 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.554.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.554 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.554.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.554 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.554.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.554 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.554.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.554 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.554.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.554 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.554.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.554 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.554.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.554 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.554.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.554 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.554.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.555.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.555.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.555 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.555.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.555 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.555.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.555 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.555.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.555 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.555.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.555 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.555.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.555 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.555.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.555 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.555.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.555 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.555.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.555 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.555.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.555 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.555.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:2 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.556.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.556.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.556 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.556.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.556 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.556.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.556 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.556.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.556 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.556.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.556 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.556.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.556 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.556.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.556 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.556.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.556 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.556.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.556 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.556.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.556 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.556.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.557.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.557.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.557 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.557.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.557 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.557.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.557 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.557.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.557 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.557.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.557 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.557.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.557 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.557.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.557 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.557.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.557 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.557.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.557 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.557.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.557 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.557.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.558.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.558.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.558 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.558.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.558 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.558.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.558 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.558.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.558 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.558.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.558 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.558.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.558 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.558.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.558 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.558.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:8 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.558 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.558.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.558 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.558.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.558 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.558.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:4 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.559.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.559.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.559 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.559.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.559 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.559.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.559 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.559.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.559 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.559.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.559 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.559.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.559 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.559.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.559 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.559.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.559 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.559.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.559 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.559.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.559 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/55/PGA_scaffold34__164_contigs__length_87950420.559.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.560.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.560.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.560 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.560.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.560 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.560.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.560 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.560.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.560 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.560.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.560 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.560.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.560 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.560.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.560 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.560.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.560 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.560.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.560 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.560.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.560 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.560.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.561.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.561.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.561 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.561.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.561 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.561.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.561 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.561.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.561 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.561.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.561 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.561.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.561 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.561.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.561 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.561.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.561 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.561.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.561 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.561.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.561 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.561.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.562.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.562.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.562 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.562.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.562 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.562.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.562 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.562.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.562 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.562.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.562 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.562.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.562 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.562.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.562 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.562.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.562 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.562.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.562 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.562.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.562 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.562.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.563.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.563.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.563 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.563.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.563 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.563.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.563 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.563.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.563 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.563.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.563 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.563.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.563 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.563.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.563 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.563.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.563 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.563.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.563 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.563.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.563 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.563.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.564.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.564.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.564 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.564.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.564 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.564.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.564 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.564.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.564 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.564.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.564 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.564.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.564 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.564.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.564 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.564.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.564 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.564.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.564 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.564.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.564 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.564.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.565.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.565.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.565 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.565.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.565 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.565.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.565 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.565.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.565 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.565.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.565 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.565.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.565 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.565.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.565 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.565.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.565 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.565.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.565 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.565.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.565 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.565.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.566.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.566.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.566 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.566.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.566 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.566.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.566 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.566.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.566 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.566.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.566 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.566.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.566 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.566.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.566 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.566.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.566 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.566.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.566 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.566.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.566 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.566.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.567.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.567.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.567 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.567.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.567 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.567.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.567 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.567.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.567 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.567.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.567 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.567.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.567 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.567.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.567 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.567.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.567 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.567.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.567 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.567.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.567 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.567.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.568.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.568.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.568 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.568.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.568 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.568.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.568 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.568.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.568 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.568.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.568 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.568.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.568 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.568.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.568 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.568.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.568 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.568.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.568 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.568.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.568 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.568.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.569.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.569.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.569 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.569.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.569 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.569.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.569 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.569.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.569 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.569.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.569 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.569.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.569 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.569.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.569 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.569.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.569 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.569.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.569 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.569.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.569 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/56/PGA_scaffold34__164_contigs__length_87950420.569.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.570.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.570.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.570 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.570.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.570 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.570.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.570 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.570.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.570 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.570.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.570 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.570.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.570 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.570.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.570 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.570.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.570 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.570.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.570 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.570.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.570 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.570.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.571.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.571.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.571 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.571.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.571 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.571.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.571 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.571.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.571 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.571.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.571 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.571.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.571 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.571.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.571 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.571.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.571 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.571.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.571 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.571.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.571 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.571.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.572.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.572.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.572 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.572.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:8 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.572 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.572.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:8 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.572 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.572.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.572 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.572.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.572 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.572.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:8 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.572 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.572.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.572 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.572.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.572 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.572.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.572 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.572.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.572 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.572.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:5 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.573.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.573.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.573 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.573.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.573 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.573.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.573 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.573.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.573 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.573.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.573 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.573.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.573 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.573.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.573 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.573.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.573 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.573.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.573 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.573.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.573 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.573.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.574.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.574.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.574 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.574.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.574 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.574.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.574 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.574.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.574 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.574.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.574 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.574.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.574 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.574.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.574 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.574.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.574 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.574.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.574 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.574.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.574 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.574.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.575.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.575.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.575 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.575.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.575 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.575.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.575 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.575.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.575 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.575.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.575 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.575.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.575 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.575.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.575 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.575.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.575 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.575.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.575 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.575.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.575 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.575.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.576.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.576.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.576 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.576.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.576 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.576.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.576 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.576.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.576 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.576.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.576 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.576.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.576 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.576.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.576 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.576.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.576 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.576.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.576 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.576.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.576 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.576.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.577.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.577.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.577 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.577.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.577 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.577.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.577 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.577.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.577 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.577.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.577 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.577.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.577 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.577.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.577 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.577.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.577 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.577.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.577 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.577.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.577 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.577.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.578.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.578.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.578 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.578.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.578 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.578.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.578 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.578.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.578 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.578.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.578 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.578.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.578 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.578.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.578 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.578.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.578 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.578.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.578 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.578.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.578 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.578.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.579.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.579.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.579 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.579.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.579 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.579.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.579 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.579.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.579 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.579.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.579 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.579.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.579 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.579.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.579 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.579.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.579 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.579.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.579 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.579.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.579 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/57/PGA_scaffold34__164_contigs__length_87950420.579.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.580.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.580.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.580 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.580.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.580 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.580.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.580 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.580.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.580 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.580.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.580 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.580.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.580 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.580.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.580 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.580.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.580 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.580.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.580 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.580.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.580 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.580.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.581.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.581.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.581 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.581.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.581 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.581.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.581 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.581.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.581 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.581.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.581 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.581.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.581 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.581.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.581 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.581.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.581 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.581.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.581 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.581.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.581 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.581.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.582.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.582.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.582 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.582.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.582 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.582.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.582 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.582.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.582 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.582.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.582 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.582.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.582 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.582.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.582 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.582.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.582 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.582.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.582 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.582.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.582 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.582.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.583.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.583.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.583 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.583.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.583 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.583.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.583 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.583.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.583 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.583.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.583 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.583.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.583 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.583.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.583 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.583.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.583 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.583.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.583 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.583.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.583 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.583.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.584.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.584.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.584 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.584.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.584 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.584.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.584 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.584.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.584 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.584.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.584 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.584.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.584 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.584.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.584 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.584.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.584 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.584.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.584 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.584.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.584 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.584.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.585.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.585.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.585 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.585.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.585 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.585.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.585 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.585.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.585 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.585.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.585 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.585.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.585 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.585.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.585 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.585.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.585 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.585.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.585 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.585.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.585 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.585.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.586.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.586.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.586 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.586.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.586 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.586.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.586 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.586.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.586 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.586.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.586 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.586.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.586 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.586.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.586 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.586.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.586 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.586.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.586 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.586.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.586 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.586.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.587.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.587.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.587 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.587.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.587 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.587.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.587 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.587.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.587 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.587.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.587 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.587.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.587 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.587.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.587 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.587.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.587 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.587.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.587 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.587.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.587 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.587.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.588.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.588.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.588 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.588.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.588 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.588.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.588 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.588.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.588 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.588.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.588 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.588.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.588 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.588.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.588 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.588.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.588 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.588.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.588 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.588.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.588 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.588.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.589.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.589.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.589 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.589.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.589 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.589.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.589 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.589.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.589 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.589.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.589 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.589.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.589 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.589.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.589 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.589.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.589 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.589.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.589 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.589.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.589 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/58/PGA_scaffold34__164_contigs__length_87950420.589.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.590.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.590.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.590 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.590.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.590 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.590.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.590 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.590.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.590 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.590.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.590 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.590.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.590 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.590.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.590 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.590.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.590 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.590.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.590 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.590.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.590 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.590.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.591.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.591.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.591 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.591.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.591 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.591.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.591 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.591.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.591 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.591.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.591 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.591.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.591 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.591.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.591 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.591.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.591 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.591.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.591 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.591.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.591 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.591.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.592.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.592.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.592 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.592.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.592 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.592.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.592 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.592.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.592 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.592.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.592 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.592.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.592 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.592.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.592 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.592.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.592 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.592.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.592 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.592.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.592 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.592.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.593.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.593.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.593 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.593.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.593 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.593.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.593 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.593.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.593 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.593.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.593 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.593.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.593 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.593.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.593 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.593.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.593 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.593.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.593 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.593.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.593 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.593.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.594.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.594.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.594 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.594.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.594 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.594.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.594 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.594.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.594 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.594.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.594 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.594.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.594 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.594.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.594 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.594.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.594 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.594.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.594 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.594.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.594 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.594.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:2 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.595.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.595.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.595 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.595.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.595 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.595.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.595 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.595.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.595 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.595.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.595 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.595.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.595 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.595.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.595 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.595.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.595 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.595.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.595 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.595.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.595 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.595.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.596.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.596.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.596 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.596.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.596 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.596.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.596 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.596.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.596 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.596.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.596 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.596.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.596 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.596.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.596 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.596.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.596 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.596.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.596 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.596.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.596 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.596.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.597.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.597.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.597 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.597.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.597 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.597.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.597 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.597.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.597 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.597.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.597 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.597.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.597 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.597.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.597 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.597.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.597 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.597.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.597 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.597.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.597 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.597.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.598.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.598.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.598 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.598.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.598 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.598.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.598 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.598.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.598 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.598.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.598 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.598.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.598 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.598.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.598 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.598.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.598 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.598.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.598 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.598.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.598 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.598.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.599.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.599.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.599 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.599.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.599 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.599.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.599 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.599.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.599 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.599.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.599 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.599.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.599 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.599.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.599 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.599.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.599 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.599.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.599 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.599.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.599 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/59/PGA_scaffold34__164_contigs__length_87950420.599.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.600.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.600.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.600 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.600.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.600 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.600.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.600 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.600.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.600 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.600.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.600 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.600.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.600 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.600.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.600 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.600.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.600 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.600.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.600 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.600.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.600 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.600.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.601.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.601.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.601 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.601.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.601 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.601.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.601 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.601.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.601 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.601.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.601 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.601.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.601 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.601.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.601 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.601.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.601 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.601.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.601 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.601.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.601 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.601.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.602.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.602.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.602 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.602.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.602 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.602.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.602 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.602.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.602 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.602.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.602 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.602.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.602 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.602.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.602 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.602.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.602 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.602.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.602 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.602.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.602 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.602.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.603.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.603.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.603 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.603.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.603 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.603.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.603 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.603.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.603 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.603.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.603 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.603.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.603 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.603.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.603 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.603.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.603 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.603.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.603 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.603.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.603 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.603.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.604.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.604.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.604 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.604.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.604 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.604.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.604 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.604.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.604 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.604.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.604 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.604.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.604 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.604.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.604 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.604.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.604 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.604.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.604 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.604.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.604 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.604.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.605.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.605.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.605 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.605.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.605 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.605.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.605 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.605.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.605 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.605.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.605 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.605.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.605 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.605.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.605 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.605.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.605 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.605.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.605 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.605.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.605 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.605.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.606.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.606.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.606 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.606.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.606 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.606.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.606 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.606.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.606 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.606.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.606 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.606.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.606 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.606.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.606 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.606.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.606 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.606.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.606 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.606.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.606 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.606.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.607.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.607.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.607 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.607.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.607 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.607.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.607 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.607.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.607 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.607.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.607 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.607.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.607 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.607.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.607 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.607.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.607 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.607.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.607 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.607.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.607 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.607.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.608.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.608.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.608 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.608.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.608 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.608.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.608 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.608.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.608 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.608.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.608 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.608.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.608 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.608.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.608 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.608.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.608 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.608.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.608 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.608.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.608 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.608.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.609.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.609.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.609 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.609.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.609 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.609.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.609 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.609.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.609 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.609.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.609 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.609.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.609 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.609.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.609 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.609.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.609 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.609.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.609 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.609.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.609 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/60/PGA_scaffold34__164_contigs__length_87950420.609.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:6 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.610.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.610.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.610 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.610.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.610 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.610.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.610 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.610.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.610 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.610.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.610 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.610.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.610 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.610.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.610 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.610.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.610 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.610.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.610 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.610.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.610 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.610.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.611.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.611.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.611 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.611.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.611 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.611.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.611 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.611.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.611 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.611.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.611 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.611.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.611 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.611.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.611 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.611.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.611 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.611.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.611 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.611.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.611 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.611.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.612.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.612.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.612 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.612.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.612 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.612.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.612 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.612.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.612 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.612.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.612 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.612.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.612 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.612.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.612 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.612.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.612 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.612.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.612 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.612.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.612 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.612.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.613.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.613.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.613 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.613.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.613 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.613.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.613 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.613.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.613 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.613.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.613 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.613.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.613 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.613.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.613 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.613.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.613 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.613.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.613 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.613.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.613 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.613.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.614.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.614.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.614 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.614.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.614 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.614.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.614 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.614.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.614 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.614.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.614 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.614.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.614 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.614.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.614 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.614.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.614 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.614.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.614 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.614.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.614 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.614.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.615.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.615.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.615 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.615.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.615 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.615.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.615 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.615.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.615 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.615.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.615 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.615.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.615 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.615.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.615 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.615.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.615 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.615.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.615 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.615.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.615 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.615.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:3 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.616.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.616.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.616 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.616.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.616 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.616.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.616 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.616.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.616 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.616.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.616 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.616.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.616 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.616.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.616 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.616.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.616 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.616.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.616 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.616.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.616 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.616.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.617.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.617.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.617 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.617.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.617 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.617.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.617 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.617.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.617 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.617.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.617 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.617.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.617 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.617.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.617 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.617.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.617 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.617.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.617 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.617.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.617 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.617.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.618.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.618.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.618 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.618.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.618 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.618.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.618 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.618.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.618 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.618.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.618 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.618.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.618 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.618.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.618 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.618.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.618 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.618.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.618 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.618.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.618 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.618.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.619.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.619.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.619 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.619.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.619 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.619.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.619 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.619.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.619 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.619.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.619 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.619.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.619 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.619.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.619 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.619.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.619 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.619.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.619 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.619.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.619 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/61/PGA_scaffold34__164_contigs__length_87950420.619.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.620.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.620.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.620 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.620.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.620 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.620.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.620 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.620.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.620 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.620.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.620 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.620.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.620 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.620.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.620 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.620.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.620 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.620.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.620 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.620.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.620 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.620.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.621.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.621.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.621 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.621.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.621 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.621.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.621 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.621.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.621 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.621.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.621 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.621.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.621 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.621.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.621 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.621.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.621 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.621.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.621 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.621.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.621 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.621.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.622.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.622.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.622 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.622.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.622 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.622.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.622 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.622.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.622 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.622.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.622 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.622.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.622 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.622.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.622 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.622.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.622 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.622.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.622 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.622.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.622 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.622.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.623.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.623.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.623 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.623.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.623 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.623.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.623 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.623.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.623 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.623.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.623 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.623.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.623 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.623.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.623 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.623.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.623 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.623.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.623 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.623.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.623 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.623.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.624.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.624.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.624 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.624.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.624 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.624.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.624 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.624.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.624 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.624.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.624 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.624.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.624 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.624.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.624 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.624.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.624 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.624.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.624 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.624.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.624 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.624.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.625.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.625.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.625 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.625.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.625 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.625.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.625 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.625.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.625 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.625.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.625 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.625.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.625 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.625.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.625 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.625.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.625 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.625.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.625 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.625.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.625 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.625.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.626.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.626.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.626 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.626.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.626 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.626.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.626 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.626.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.626 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.626.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.626 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.626.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.626 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.626.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.626 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.626.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.626 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.626.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.626 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.626.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.626 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.626.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.627.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.627.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.627 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.627.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.627 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.627.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.627 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.627.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.627 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.627.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.627 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.627.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.627 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.627.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.627 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.627.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.627 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.627.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.627 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.627.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.627 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.627.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.628.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.628.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.628 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.628.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.628 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.628.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.628 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.628.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.628 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.628.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.628 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.628.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.628 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.628.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.628 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.628.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.628 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.628.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.628 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.628.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.628 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.628.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.629.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.629.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.629 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.629.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.629 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.629.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.629 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.629.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.629 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.629.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.629 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.629.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.629 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.629.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.629 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.629.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.629 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.629.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.629 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.629.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.629 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/62/PGA_scaffold34__164_contigs__length_87950420.629.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:2 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.630.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.630.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.630 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.630.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.630 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.630.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.630 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.630.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.630 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.630.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.630 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.630.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.630 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.630.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.630 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.630.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.630 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.630.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.630 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.630.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.630 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.630.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.631.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.631.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.631 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.631.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.631 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.631.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.631 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.631.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.631 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.631.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.631 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.631.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.631 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.631.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.631 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.631.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.631 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.631.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.631 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.631.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.631 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.631.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.632.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.632.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.632 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.632.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.632 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.632.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.632 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.632.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.632 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.632.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.632 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.632.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.632 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.632.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.632 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.632.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.632 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.632.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.632 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.632.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.632 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.632.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.633.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.633.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.633 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.633.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:10 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.633 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.633.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.633 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.633.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.633 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.633.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.633 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.633.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:10 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.633 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.633.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.633 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.633.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:8 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.633 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.633.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.633 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.633.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.633 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.633.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:5 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.634.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.634.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.634 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.634.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.634 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.634.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.634 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.634.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.634 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.634.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.634 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.634.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.634 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.634.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.634 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.634.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.634 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.634.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.634 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.634.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.634 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.634.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.635.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.635.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.635 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.635.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.635 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.635.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.635 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.635.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.635 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.635.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.635 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.635.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.635 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.635.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.635 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.635.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.635 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.635.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.635 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.635.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.635 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.635.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.636.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.636.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.636 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.636.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.636 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.636.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.636 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.636.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.636 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.636.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.636 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.636.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.636 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.636.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.636 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.636.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.636 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.636.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.636 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.636.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.636 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.636.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.637.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.637.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.637 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.637.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.637 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.637.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.637 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.637.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.637 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.637.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.637 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.637.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.637 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.637.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.637 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.637.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.637 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.637.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.637 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.637.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.637 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.637.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.638.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.638.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.638 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.638.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.638 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.638.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.638 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.638.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.638 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.638.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.638 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.638.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.638 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.638.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.638 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.638.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.638 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.638.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.638 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.638.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.638 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.638.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.639.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.639.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.639 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.639.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.639 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.639.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.639 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.639.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.639 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.639.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.639 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.639.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.639 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.639.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.639 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.639.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.639 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.639.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.639 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.639.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.639 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/63/PGA_scaffold34__164_contigs__length_87950420.639.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.640.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.640.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.640 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.640.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.640 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.640.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.640 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.640.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.640 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.640.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.640 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.640.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.640 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.640.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.640 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.640.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.640 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.640.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.640 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.640.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.640 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.640.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.641.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.641.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.641 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.641.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.641 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.641.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.641 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.641.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.641 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.641.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.641 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.641.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.641 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.641.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.641 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.641.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.641 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.641.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.641 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.641.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.641 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.641.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.642.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.642.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.642 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.642.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.642 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.642.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.642 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.642.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.642 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.642.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.642 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.642.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.642 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.642.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.642 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.642.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.642 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.642.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.642 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.642.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.642 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.642.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.643.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.643.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.643 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.643.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.643 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.643.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.643 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.643.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.643 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.643.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.643 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.643.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.643 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.643.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.643 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.643.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.643 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.643.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.643 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.643.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.643 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.643.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.644.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.644.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.644 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.644.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.644 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.644.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.644 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.644.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.644 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.644.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.644 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.644.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.644 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.644.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.644 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.644.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.644 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.644.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.644 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.644.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.644 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.644.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.645.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.645.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.645 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.645.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.645 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.645.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.645 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.645.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.645 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.645.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.645 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.645.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.645 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.645.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.645 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.645.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.645 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.645.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.645 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.645.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.645 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.645.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.646.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.646.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.646 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.646.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.646 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.646.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.646 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.646.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.646 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.646.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.646 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.646.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.646 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.646.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.646 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.646.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.646 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.646.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.646 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.646.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.646 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.646.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.647.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.647.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.647 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.647.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.647 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.647.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.647 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.647.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.647 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.647.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.647 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.647.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.647 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.647.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.647 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.647.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.647 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.647.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.647 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.647.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.647 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.647.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.648.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.648.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.648 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.648.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.648 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.648.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.648 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.648.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.648 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.648.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.648 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.648.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.648 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.648.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.648 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.648.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.648 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.648.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.648 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.648.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.648 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.648.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.649.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.649.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.649 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.649.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.649 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.649.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.649 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.649.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.649 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.649.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.649 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.649.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.649 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.649.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.649 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.649.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.649 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.649.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.649 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.649.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.649 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/64/PGA_scaffold34__164_contigs__length_87950420.649.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.650.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.650.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.650 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.650.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.650 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.650.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.650 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.650.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.650 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.650.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.650 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.650.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:8 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.650 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.650.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.650 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.650.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:8 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.650 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.650.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.650 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.650.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.650 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.650.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.651.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.651.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.651 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.651.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.651 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.651.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.651 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.651.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.651 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.651.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.651 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.651.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.651 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.651.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.651 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.651.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.651 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.651.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.651 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.651.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.651 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.651.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.652.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.652.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.652 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.652.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.652 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.652.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.652 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.652.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.652 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.652.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.652 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.652.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.652 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.652.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.652 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.652.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.652 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.652.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.652 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.652.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.652 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.652.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.653.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.653.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.653 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.653.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.653 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.653.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.653 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.653.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.653 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.653.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.653 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.653.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.653 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.653.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.653 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.653.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.653 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.653.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.653 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.653.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.653 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.653.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.654.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.654.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.654 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.654.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.654 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.654.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.654 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.654.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.654 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.654.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.654 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.654.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.654 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.654.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.654 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.654.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.654 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.654.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.654 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.654.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.654 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.654.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.655.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.655.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.655 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.655.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.655 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.655.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.655 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.655.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.655 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.655.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.655 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.655.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.655 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.655.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.655 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.655.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.655 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.655.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.655 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.655.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.655 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.655.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.656.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.656.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.656 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.656.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.656 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.656.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.656 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.656.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.656 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.656.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.656 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.656.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.656 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.656.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.656 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.656.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.656 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.656.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.656 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.656.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.656 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.656.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.657.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.657.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.657 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.657.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.657 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.657.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.657 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.657.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.657 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.657.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.657 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.657.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.657 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.657.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.657 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.657.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.657 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.657.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.657 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.657.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.657 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.657.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.658.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.658.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.658 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.658.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.658 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.658.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.658 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.658.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.658 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.658.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:13 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.658 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.658.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.658 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.658.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.658 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.658.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:11 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.658 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.658.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.658 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.658.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:8 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.658 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.658.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:3 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.659.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.659.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.659 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.659.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.659 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.659.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.659 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.659.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.659 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.659.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.659 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.659.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.659 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.659.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.659 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.659.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.659 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.659.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.659 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.659.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.659 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/65/PGA_scaffold34__164_contigs__length_87950420.659.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:2 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.660.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.660.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.660 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.660.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.660 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.660.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.660 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.660.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.660 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.660.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.660 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.660.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.660 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.660.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.660 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.660.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.660 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.660.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.660 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.660.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.660 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.660.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.661.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.661.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.661 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.661.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.661 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.661.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.661 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.661.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.661 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.661.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.661 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.661.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.661 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.661.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.661 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.661.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.661 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.661.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.661 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.661.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.661 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.661.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.662.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.662.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.662 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.662.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.662 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.662.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.662 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.662.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.662 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.662.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.662 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.662.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.662 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.662.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.662 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.662.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.662 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.662.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.662 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.662.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.662 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.662.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:2 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.663.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.663.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.663 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.663.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.663 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.663.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.663 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.663.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.663 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.663.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.663 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.663.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.663 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.663.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.663 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.663.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.663 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.663.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.663 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.663.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.663 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.663.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.664.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.664.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.664 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.664.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.664 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.664.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.664 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.664.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.664 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.664.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.664 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.664.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.664 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.664.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.664 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.664.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.664 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.664.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.664 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.664.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.664 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.664.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.665.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.665.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.665 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.665.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.665 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.665.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.665 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.665.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.665 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.665.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.665 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.665.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.665 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.665.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:8 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.665 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.665.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:11 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.665 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.665.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.665 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.665.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.665 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.665.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:9 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.666.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.666.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.666 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.666.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.666 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.666.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.666 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.666.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.666 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.666.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.666 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.666.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.666 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.666.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.666 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.666.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.666 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.666.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.666 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.666.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.666 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.666.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.667.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.667.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.667 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.667.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.667 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.667.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.667 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.667.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.667 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.667.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.667 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.667.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.667 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.667.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.667 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.667.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.667 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.667.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.667 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.667.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.667 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.667.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.668.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.668.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.668 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.668.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.668 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.668.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.668 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.668.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.668 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.668.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.668 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.668.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.668 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.668.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.668 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.668.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.668 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.668.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.668 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.668.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.668 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.668.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.669.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.669.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.669 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.669.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.669 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.669.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.669 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.669.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.669 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.669.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.669 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.669.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.669 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.669.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.669 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.669.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.669 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.669.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.669 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.669.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.669 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/66/PGA_scaffold34__164_contigs__length_87950420.669.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.670.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.670.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.670 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.670.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.670 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.670.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.670 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.670.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.670 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.670.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.670 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.670.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.670 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.670.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.670 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.670.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.670 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.670.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.670 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.670.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.670 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.670.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.671.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.671.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.671 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.671.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.671 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.671.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.671 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.671.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.671 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.671.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.671 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.671.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.671 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.671.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.671 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.671.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.671 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.671.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.671 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.671.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.671 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.671.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.672.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.672.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.672 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.672.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.672 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.672.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.672 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.672.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.672 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.672.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.672 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.672.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.672 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.672.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.672 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.672.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.672 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.672.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.672 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.672.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.672 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.672.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.673.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.673.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.673 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.673.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.673 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.673.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.673 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.673.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.673 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.673.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.673 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.673.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.673 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.673.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.673 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.673.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.673 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.673.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.673 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.673.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.673 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.673.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.674.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.674.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.674 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.674.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.674 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.674.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.674 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.674.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.674 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.674.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.674 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.674.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.674 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.674.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.674 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.674.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.674 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.674.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.674 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.674.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.674 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.674.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.675.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.675.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.675 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.675.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.675 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.675.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.675 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.675.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.675 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.675.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.675 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.675.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.675 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.675.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.675 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.675.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.675 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.675.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.675 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.675.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.675 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.675.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.676.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.676.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.676 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.676.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.676 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.676.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.676 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.676.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.676 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.676.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.676 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.676.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.676 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.676.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.676 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.676.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.676 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.676.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.676 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.676.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.676 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.676.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.677.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.677.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.677 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.677.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.677 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.677.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.677 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.677.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.677 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.677.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.677 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.677.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.677 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.677.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.677 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.677.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.677 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.677.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.677 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.677.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.677 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.677.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.678.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.678.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.678 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.678.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:8 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.678 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.678.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.678 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.678.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.678 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.678.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.678 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.678.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:8 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.678 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.678.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:7 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.678 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.678.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.678 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.678.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.678 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.678.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.678 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.678.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:3 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.679.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.679.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.679 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.679.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.679 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.679.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.679 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.679.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.679 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.679.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.679 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.679.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.679 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.679.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.679 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.679.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.679 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.679.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.679 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.679.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.679 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/67/PGA_scaffold34__164_contigs__length_87950420.679.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.680.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.680.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.680 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.680.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.680 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.680.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.680 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.680.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.680 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.680.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.680 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.680.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.680 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.680.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.680 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.680.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.680 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.680.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.680 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.680.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.680 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.680.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.681.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.681.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.681 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.681.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.681 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.681.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.681 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.681.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.681 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.681.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.681 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.681.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.681 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.681.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.681 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.681.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.681 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.681.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.681 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.681.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.681 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.681.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.682.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.682.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.682 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.682.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:864 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.682 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.682.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:792 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.682 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.682.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:803 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.682 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.682.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:803 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.682 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.682.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:817 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.682 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.682.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:862 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.682 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.682.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:802 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.682 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.682.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:815 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.682 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.682.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:804 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.682 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.682.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:819 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.683.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.683.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.683 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.683.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.683 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.683.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.683 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.683.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.683 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.683.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.683 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.683.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.683 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.683.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.683 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.683.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.683 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.683.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.683 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.683.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.683 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.683.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.684.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.684.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.684 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.684.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.684 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.684.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.684 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.684.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.684 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.684.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.684 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.684.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.684 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.684.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.684 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.684.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.684 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.684.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.684 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.684.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.684 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.684.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.685.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.685.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.685 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.685.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.685 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.685.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.685 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.685.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.685 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.685.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.685 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.685.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.685 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.685.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.685 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.685.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.685 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.685.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.685 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.685.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.685 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.685.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.686.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.686.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.686 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.686.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.686 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.686.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.686 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.686.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.686 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.686.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.686 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.686.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.686 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.686.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.686 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.686.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.686 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.686.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.686 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.686.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.686 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.686.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.687.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.687.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.687 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.687.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.687 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.687.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.687 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.687.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.687 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.687.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.687 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.687.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.687 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.687.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.687 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.687.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.687 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.687.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.687 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.687.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.687 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.687.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.688.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.688.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.688 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.688.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.688 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.688.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.688 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.688.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.688 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.688.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.688 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.688.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.688 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.688.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.688 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.688.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.688 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.688.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.688 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.688.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.688 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.688.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.689.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.689.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.689 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.689.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.689 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.689.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.689 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.689.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.689 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.689.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.689 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.689.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.689 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.689.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.689 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.689.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.689 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.689.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.689 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.689.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.689 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/68/PGA_scaffold34__164_contigs__length_87950420.689.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.690.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.690.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.690 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.690.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.690 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.690.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.690 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.690.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.690 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.690.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.690 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.690.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.690 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.690.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.690 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.690.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.690 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.690.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.690 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.690.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.690 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.690.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.691.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.691.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.691 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.691.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.691 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.691.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.691 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.691.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.691 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.691.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.691 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.691.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.691 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.691.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.691 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.691.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.691 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.691.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.691 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.691.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.691 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.691.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.692.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.692.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.692 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.692.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.692 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.692.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.692 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.692.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.692 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.692.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.692 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.692.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.692 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.692.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.692 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.692.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.692 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.692.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.692 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.692.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.692 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.692.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.693.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.693.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.693 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.693.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.693 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.693.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.693 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.693.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.693 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.693.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.693 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.693.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.693 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.693.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.693 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.693.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.693 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.693.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.693 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.693.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.693 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.693.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.694.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.694.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.694 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.694.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.694 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.694.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.694 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.694.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.694 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.694.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.694 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.694.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.694 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.694.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.694 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.694.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.694 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.694.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.694 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.694.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.694 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.694.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.695.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.695.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.695 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.695.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.695 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.695.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.695 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.695.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.695 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.695.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.695 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.695.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.695 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.695.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.695 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.695.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.695 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.695.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.695 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.695.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.695 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.695.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.696.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.696.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.696 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.696.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.696 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.696.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.696 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.696.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.696 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.696.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.696 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.696.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.696 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.696.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.696 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.696.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.696 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.696.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.696 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.696.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.696 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.696.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.697.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.697.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.697 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.697.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.697 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.697.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.697 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.697.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.697 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.697.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.697 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.697.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.697 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.697.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.697 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.697.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.697 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.697.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.697 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.697.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.697 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.697.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.698.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.698.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.698 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.698.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.698 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.698.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.698 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.698.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.698 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.698.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.698 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.698.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.698 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.698.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.698 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.698.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.698 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.698.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.698 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.698.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.698 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.698.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.699.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.699.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.699 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.699.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.699 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.699.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.699 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.699.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.699 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.699.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.699 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.699.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.699 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.699.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.699 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.699.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.699 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.699.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.699 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.699.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.699 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/69/PGA_scaffold34__164_contigs__length_87950420.699.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.700.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.700.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.700 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.700.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.700 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.700.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.700 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.700.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.700 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.700.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.700 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.700.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.700 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.700.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.700 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.700.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.700 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.700.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.700 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.700.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.700 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.700.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.701.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.701.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.701 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.701.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.701 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.701.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.701 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.701.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.701 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.701.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.701 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.701.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.701 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.701.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.701 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.701.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.701 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.701.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.701 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.701.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.701 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.701.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.702.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.702.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.702 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.702.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.702 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.702.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.702 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.702.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.702 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.702.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.702 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.702.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.702 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.702.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.702 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.702.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.702 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.702.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.702 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.702.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.702 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.702.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.703.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.703.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.703 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.703.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.703 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.703.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.703 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.703.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.703 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.703.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.703 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.703.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.703 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.703.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.703 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.703.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.703 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.703.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.703 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.703.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.703 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.703.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.704.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.704.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.704 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.704.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.704 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.704.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.704 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.704.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.704 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.704.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.704 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.704.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.704 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.704.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.704 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.704.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.704 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.704.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.704 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.704.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.704 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.704.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.705.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.705.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.705 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.705.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.705 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.705.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.705 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.705.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.705 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.705.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.705 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.705.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.705 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.705.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.705 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.705.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.705 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.705.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.705 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.705.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.705 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.705.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.706.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.706.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.706 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.706.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.706 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.706.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.706 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.706.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.706 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.706.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.706 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.706.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.706 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.706.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.706 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.706.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.706 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.706.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.706 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.706.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.706 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.706.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.707.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.707.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.707 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.707.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.707 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.707.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.707 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.707.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.707 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.707.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.707 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.707.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.707 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.707.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.707 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.707.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.707 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.707.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.707 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.707.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.707 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.707.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.708.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.708.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.708 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.708.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.708 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.708.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.708 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.708.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.708 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.708.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.708 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.708.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.708 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.708.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.708 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.708.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.708 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.708.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.708 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.708.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.708 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.708.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.709.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.709.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.709 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.709.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.709 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.709.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.709 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.709.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.709 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.709.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.709 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.709.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.709 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.709.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.709 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.709.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.709 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.709.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.709 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.709.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.709 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/70/PGA_scaffold34__164_contigs__length_87950420.709.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.710.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.710.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.710 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.710.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.710 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.710.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.710 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.710.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.710 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.710.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.710 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.710.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.710 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.710.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.710 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.710.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.710 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.710.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.710 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.710.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.710 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.710.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.711.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.711.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.711 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.711.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.711 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.711.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.711 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.711.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.711 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.711.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.711 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.711.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.711 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.711.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.711 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.711.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.711 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.711.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.711 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.711.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.711 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.711.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.712.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.712.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.712 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.712.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.712 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.712.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.712 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.712.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.712 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.712.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.712 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.712.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.712 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.712.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.712 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.712.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.712 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.712.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.712 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.712.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.712 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.712.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.713.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.713.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.713 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.713.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.713 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.713.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.713 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.713.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.713 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.713.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.713 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.713.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.713 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.713.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.713 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.713.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.713 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.713.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.713 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.713.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.713 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.713.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.714.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.714.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.714 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.714.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.714 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.714.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.714 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.714.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.714 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.714.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.714 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.714.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.714 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.714.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.714 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.714.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.714 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.714.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.714 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.714.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.714 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.714.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.715.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.715.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.715 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.715.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.715 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.715.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.715 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.715.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.715 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.715.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.715 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.715.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.715 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.715.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.715 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.715.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.715 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.715.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.715 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.715.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.715 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.715.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.716.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.716.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.716 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.716.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.716 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.716.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.716 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.716.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.716 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.716.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.716 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.716.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.716 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.716.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.716 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.716.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.716 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.716.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.716 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.716.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.716 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.716.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.717.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.717.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.717 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.717.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.717 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.717.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.717 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.717.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.717 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.717.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.717 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.717.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.717 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.717.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.717 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.717.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.717 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.717.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.717 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.717.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.717 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.717.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.718.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.718.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.718 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.718.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.718 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.718.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.718 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.718.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.718 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.718.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.718 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.718.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.718 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.718.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.718 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.718.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.718 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.718.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.718 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.718.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.718 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.718.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.719.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.719.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.719 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.719.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.719 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.719.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.719 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.719.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.719 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.719.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.719 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.719.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.719 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.719.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.719 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.719.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.719 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.719.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.719 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.719.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.719 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/71/PGA_scaffold34__164_contigs__length_87950420.719.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.720.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.720.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.720 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.720.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.720 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.720.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.720 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.720.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.720 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.720.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.720 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.720.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.720 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.720.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.720 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.720.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.720 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.720.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.720 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.720.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.720 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.720.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.721.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.721.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.721 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.721.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.721 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.721.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.721 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.721.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.721 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.721.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.721 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.721.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.721 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.721.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.721 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.721.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.721 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.721.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.721 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.721.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.721 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.721.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.722.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.722.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.722 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.722.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.722 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.722.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.722 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.722.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.722 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.722.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.722 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.722.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.722 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.722.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.722 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.722.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.722 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.722.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.722 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.722.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.722 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.722.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.723.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.723.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.723 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.723.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.723 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.723.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.723 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.723.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.723 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.723.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.723 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.723.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.723 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.723.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.723 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.723.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.723 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.723.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.723 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.723.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.723 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.723.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.724.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.724.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.724 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.724.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.724 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.724.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.724 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.724.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.724 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.724.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.724 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.724.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.724 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.724.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.724 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.724.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.724 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.724.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.724 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.724.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.724 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.724.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.725.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.725.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.725 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.725.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.725 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.725.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.725 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.725.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.725 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.725.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.725 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.725.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.725 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.725.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.725 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.725.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.725 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.725.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.725 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.725.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.725 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.725.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.726.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.726.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.726 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.726.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.726 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.726.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.726 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.726.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.726 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.726.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.726 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.726.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.726 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.726.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.726 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.726.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.726 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.726.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.726 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.726.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.726 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.726.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.727.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.727.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.727 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.727.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.727 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.727.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.727 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.727.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.727 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.727.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.727 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.727.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.727 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.727.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.727 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.727.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.727 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.727.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.727 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.727.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.727 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.727.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.728.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.728.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.728 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.728.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.728 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.728.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.728 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.728.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.728 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.728.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.728 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.728.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.728 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.728.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.728 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.728.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.728 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.728.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.728 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.728.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.728 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.728.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.729.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.729.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.729 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.729.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.729 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.729.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.729 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.729.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.729 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.729.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.729 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.729.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.729 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.729.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.729 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.729.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.729 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.729.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.729 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.729.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.729 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/72/PGA_scaffold34__164_contigs__length_87950420.729.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.730.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.730.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.730 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.730.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.730 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.730.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.730 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.730.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.730 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.730.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.730 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.730.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.730 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.730.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.730 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.730.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.730 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.730.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.730 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.730.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.730 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.730.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.731.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.731.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.731 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.731.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.731 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.731.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.731 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.731.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.731 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.731.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.731 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.731.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.731 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.731.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.731 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.731.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.731 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.731.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.731 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.731.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.731 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.731.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.732.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.732.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.732 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.732.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.732 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.732.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.732 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.732.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.732 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.732.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.732 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.732.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.732 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.732.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.732 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.732.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.732 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.732.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.732 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.732.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.732 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.732.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.733.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.733.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.733 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.733.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.733 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.733.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.733 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.733.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.733 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.733.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.733 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.733.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.733 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.733.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.733 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.733.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.733 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.733.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.733 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.733.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.733 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.733.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.734.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.734.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.734 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.734.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.734 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.734.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.734 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.734.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.734 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.734.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.734 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.734.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.734 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.734.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.734 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.734.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.734 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.734.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.734 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.734.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.734 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.734.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.735.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.735.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.735 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.735.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.735 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.735.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.735 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.735.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.735 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.735.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.735 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.735.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.735 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.735.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.735 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.735.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.735 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.735.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.735 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.735.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.735 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.735.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.736.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.736.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.736 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.736.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.736 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.736.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.736 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.736.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.736 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.736.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.736 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.736.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.736 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.736.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.736 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.736.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.736 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.736.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.736 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.736.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.736 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.736.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.737.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.737.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.737 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.737.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.737 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.737.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.737 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.737.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.737 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.737.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.737 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.737.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.737 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.737.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.737 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.737.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.737 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.737.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.737 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.737.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.737 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.737.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.738.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.738.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.738 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.738.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.738 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.738.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.738 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.738.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.738 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.738.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.738 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.738.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.738 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.738.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.738 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.738.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.738 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.738.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.738 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.738.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.738 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.738.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.739.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.739.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.739 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.739.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.739 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.739.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.739 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.739.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.739 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.739.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.739 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.739.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.739 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.739.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.739 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.739.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.739 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.739.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.739 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.739.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.739 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/73/PGA_scaffold34__164_contigs__length_87950420.739.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.740.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.740.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.740 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.740.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.740 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.740.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.740 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.740.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.740 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.740.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.740 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.740.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.740 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.740.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.740 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.740.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.740 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.740.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.740 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.740.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.740 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.740.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.741.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.741.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.741 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.741.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.741 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.741.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.741 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.741.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.741 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.741.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.741 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.741.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.741 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.741.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.741 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.741.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.741 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.741.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.741 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.741.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.741 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.741.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.742.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.742.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.742 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.742.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.742 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.742.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.742 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.742.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.742 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.742.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.742 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.742.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.742 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.742.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.742 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.742.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.742 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.742.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.742 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.742.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.742 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.742.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.743.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.743.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.743 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.743.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.743 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.743.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.743 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.743.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.743 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.743.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.743 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.743.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.743 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.743.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.743 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.743.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.743 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.743.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.743 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.743.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.743 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.743.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.744.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.744.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.744 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.744.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.744 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.744.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.744 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.744.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.744 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.744.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.744 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.744.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.744 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.744.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.744 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.744.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.744 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.744.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.744 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.744.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.744 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.744.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.745.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.745.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.745 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.745.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.745 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.745.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.745 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.745.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.745 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.745.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.745 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.745.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.745 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.745.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.745 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.745.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.745 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.745.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.745 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.745.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.745 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.745.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.746.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.746.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.746 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.746.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.746 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.746.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.746 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.746.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.746 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.746.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.746 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.746.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.746 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.746.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.746 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.746.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.746 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.746.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.746 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.746.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.746 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.746.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.747.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.747.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.747 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.747.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.747 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.747.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.747 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.747.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.747 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.747.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.747 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.747.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.747 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.747.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.747 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.747.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.747 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.747.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.747 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.747.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.747 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.747.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.748.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.748.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.748 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.748.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.748 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.748.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.748 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.748.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.748 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.748.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.748 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.748.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.748 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.748.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.748 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.748.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.748 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.748.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.748 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.748.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.748 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.748.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.749.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.749.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.749 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.749.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.749 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.749.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.749 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.749.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.749 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.749.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.749 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.749.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.749 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.749.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.749 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.749.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.749 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.749.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.749 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.749.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.749 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/74/PGA_scaffold34__164_contigs__length_87950420.749.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.750.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.750.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.750 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.750.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.750 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.750.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.750 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.750.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.750 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.750.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.750 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.750.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.750 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.750.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.750 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.750.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.750 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.750.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.750 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.750.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.750 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.750.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.751.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.751.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.751 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.751.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.751 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.751.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.751 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.751.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.751 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.751.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.751 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.751.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.751 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.751.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.751 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.751.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.751 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.751.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.751 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.751.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.751 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.751.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.752.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.752.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.752 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.752.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.752 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.752.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.752 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.752.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.752 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.752.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.752 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.752.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.752 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.752.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.752 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.752.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.752 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.752.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.752 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.752.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.752 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.752.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.753.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.753.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.753 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.753.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.753 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.753.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.753 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.753.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.753 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.753.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.753 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.753.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.753 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.753.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.753 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.753.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.753 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.753.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.753 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.753.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.753 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.753.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.754.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.754.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.754 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.754.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.754 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.754.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.754 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.754.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.754 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.754.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.754 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.754.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.754 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.754.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.754 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.754.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.754 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.754.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.754 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.754.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.754 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.754.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.755.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.755.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.755 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.755.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.755 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.755.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.755 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.755.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.755 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.755.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.755 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.755.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.755 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.755.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.755 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.755.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.755 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.755.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.755 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.755.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.755 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.755.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.756.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.756.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.756 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.756.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:10 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.756 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.756.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:11 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.756 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.756.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:10 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.756 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.756.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:13 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.756 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.756.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:18 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.756 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.756.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:13 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.756 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.756.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:12 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.756 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.756.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:9 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.756 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.756.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.756 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.756.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:5 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.757.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.757.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.757 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.757.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.757 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.757.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.757 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.757.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.757 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.757.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.757 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.757.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.757 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.757.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.757 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.757.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.757 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.757.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.757 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.757.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.757 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.757.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.758.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.758.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.758 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.758.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.758 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.758.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.758 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.758.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.758 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.758.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.758 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.758.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.758 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.758.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.758 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.758.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.758 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.758.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.758 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.758.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.758 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.758.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.759.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.759.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.759 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.759.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.759 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.759.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.759 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.759.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.759 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.759.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.759 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.759.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.759 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.759.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.759 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.759.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.759 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.759.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.759 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.759.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.759 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/75/PGA_scaffold34__164_contigs__length_87950420.759.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.760.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.760.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.760 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.760.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.760 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.760.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.760 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.760.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.760 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.760.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.760 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.760.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.760 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.760.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.760 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.760.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.760 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.760.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.760 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.760.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.760 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.760.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.761.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.761.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.761 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.761.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.761 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.761.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.761 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.761.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.761 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.761.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.761 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.761.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.761 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.761.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.761 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.761.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.761 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.761.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.761 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.761.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.761 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.761.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.762.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.762.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.762 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.762.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.762 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.762.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.762 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.762.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.762 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.762.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.762 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.762.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.762 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.762.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.762 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.762.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.762 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.762.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.762 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.762.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.762 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.762.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.763.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.763.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.763 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.763.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.763 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.763.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.763 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.763.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.763 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.763.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.763 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.763.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.763 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.763.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.763 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.763.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.763 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.763.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.763 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.763.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.763 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.763.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.764.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.764.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.764 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.764.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.764 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.764.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.764 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.764.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.764 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.764.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.764 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.764.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.764 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.764.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.764 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.764.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.764 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.764.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.764 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.764.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.764 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.764.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.765.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.765.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.765 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.765.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.765 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.765.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.765 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.765.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.765 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.765.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.765 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.765.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.765 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.765.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.765 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.765.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.765 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.765.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.765 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.765.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.765 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.765.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.766.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.766.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.766 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.766.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.766 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.766.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.766 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.766.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.766 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.766.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.766 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.766.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.766 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.766.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.766 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.766.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.766 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.766.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.766 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.766.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.766 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.766.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.767.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.767.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.767 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.767.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.767 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.767.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.767 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.767.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.767 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.767.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.767 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.767.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.767 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.767.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.767 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.767.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.767 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.767.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.767 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.767.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.767 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.767.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.768.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.768.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.768 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.768.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.768 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.768.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.768 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.768.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.768 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.768.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.768 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.768.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.768 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.768.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.768 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.768.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.768 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.768.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.768 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.768.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.768 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.768.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.769.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.769.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.769 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.769.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.769 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.769.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.769 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.769.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.769 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.769.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.769 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.769.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.769 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.769.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.769 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.769.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.769 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.769.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.769 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.769.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.769 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/76/PGA_scaffold34__164_contigs__length_87950420.769.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.770.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.770.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.770 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.770.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.770 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.770.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.770 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.770.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.770 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.770.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.770 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.770.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.770 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.770.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.770 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.770.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.770 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.770.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.770 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.770.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.770 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.770.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.771.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.771.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.771 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.771.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.771 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.771.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.771 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.771.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.771 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.771.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.771 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.771.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.771 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.771.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.771 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.771.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.771 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.771.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.771 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.771.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.771 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.771.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.772.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.772.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.772 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.772.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.772 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.772.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.772 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.772.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.772 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.772.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.772 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.772.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.772 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.772.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.772 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.772.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.772 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.772.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.772 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.772.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.772 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.772.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.773.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.773.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.773 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.773.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.773 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.773.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.773 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.773.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.773 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.773.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.773 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.773.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.773 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.773.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.773 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.773.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.773 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.773.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.773 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.773.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.773 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.773.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.774.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.774.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.774 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.774.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.774 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.774.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.774 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.774.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.774 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.774.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.774 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.774.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.774 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.774.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.774 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.774.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.774 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.774.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.774 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.774.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.774 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.774.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.775.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.775.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.775 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.775.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.775 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.775.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.775 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.775.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.775 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.775.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.775 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.775.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.775 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.775.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.775 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.775.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.775 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.775.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.775 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.775.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.775 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.775.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.776.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.776.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.776 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.776.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.776 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.776.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.776 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.776.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.776 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.776.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.776 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.776.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.776 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.776.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.776 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.776.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.776 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.776.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.776 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.776.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.776 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.776.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.777.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.777.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.777 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.777.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.777 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.777.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.777 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.777.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.777 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.777.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.777 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.777.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.777 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.777.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.777 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.777.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.777 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.777.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.777 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.777.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.777 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.777.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.778.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.778.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.778 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.778.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.778 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.778.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.778 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.778.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.778 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.778.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.778 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.778.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.778 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.778.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.778 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.778.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.778 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.778.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.778 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.778.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.778 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.778.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.779.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.779.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.779 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.779.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.779 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.779.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.779 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.779.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.779 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.779.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.779 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.779.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.779 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.779.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.779 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.779.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.779 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.779.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.779 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.779.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.779 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/77/PGA_scaffold34__164_contigs__length_87950420.779.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.780.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.780.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.780 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.780.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.780 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.780.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.780 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.780.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.780 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.780.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.780 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.780.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.780 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.780.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.780 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.780.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.780 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.780.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.780 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.780.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.780 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.780.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.781.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.781.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.781 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.781.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.781 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.781.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.781 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.781.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.781 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.781.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.781 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.781.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.781 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.781.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.781 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.781.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.781 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.781.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.781 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.781.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.781 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.781.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.782.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.782.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.782 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.782.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.782 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.782.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.782 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.782.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.782 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.782.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.782 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.782.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.782 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.782.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.782 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.782.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.782 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.782.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.782 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.782.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.782 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.782.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.783.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.783.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.783 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.783.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.783 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.783.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.783 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.783.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.783 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.783.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.783 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.783.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.783 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.783.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.783 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.783.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.783 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.783.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.783 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.783.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.783 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.783.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.784.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.784.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.784 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.784.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.784 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.784.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.784 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.784.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.784 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.784.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.784 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.784.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.784 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.784.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.784 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.784.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.784 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.784.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.784 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.784.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.784 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.784.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.785.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.785.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.785 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.785.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.785 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.785.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.785 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.785.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.785 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.785.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.785 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.785.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.785 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.785.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.785 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.785.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.785 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.785.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.785 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.785.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.785 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.785.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.786.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.786.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.786 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.786.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.786 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.786.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.786 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.786.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.786 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.786.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.786 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.786.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.786 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.786.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.786 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.786.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.786 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.786.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.786 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.786.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.786 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.786.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.787.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.787.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.787 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.787.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.787 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.787.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.787 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.787.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.787 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.787.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.787 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.787.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.787 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.787.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.787 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.787.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.787 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.787.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.787 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.787.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.787 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.787.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.788.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.788.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.788 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.788.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.788 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.788.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.788 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.788.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.788 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.788.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.788 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.788.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.788 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.788.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.788 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.788.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.788 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.788.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.788 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.788.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.788 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.788.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.789.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.789.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.789 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.789.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.789 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.789.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.789 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.789.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.789 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.789.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.789 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.789.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.789 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.789.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.789 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.789.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.789 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.789.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.789 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.789.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.789 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/78/PGA_scaffold34__164_contigs__length_87950420.789.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.790.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.790.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.790 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.790.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.790 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.790.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.790 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.790.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.790 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.790.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.790 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.790.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.790 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.790.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.790 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.790.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.790 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.790.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.790 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.790.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.790 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.790.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.791.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.791.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.791 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.791.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.791 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.791.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.791 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.791.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.791 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.791.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.791 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.791.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.791 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.791.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.791 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.791.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.791 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.791.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.791 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.791.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.791 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.791.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.792.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.792.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.792 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.792.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.792 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.792.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.792 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.792.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.792 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.792.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.792 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.792.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.792 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.792.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.792 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.792.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.792 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.792.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.792 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.792.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.792 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.792.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.793.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.793.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.793 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.793.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.793 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.793.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.793 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.793.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.793 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.793.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.793 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.793.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.793 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.793.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.793 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.793.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.793 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.793.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.793 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.793.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.793 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.793.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.794.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.794.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.794 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.794.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.794 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.794.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.794 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.794.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.794 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.794.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.794 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.794.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.794 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.794.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.794 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.794.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.794 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.794.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.794 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.794.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.794 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.794.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.795.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.795.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.795 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.795.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.795 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.795.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.795 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.795.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.795 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.795.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.795 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.795.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.795 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.795.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.795 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.795.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.795 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.795.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.795 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.795.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.795 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.795.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.796.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.796.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.796 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.796.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.796 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.796.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.796 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.796.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.796 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.796.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.796 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.796.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.796 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.796.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.796 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.796.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.796 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.796.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.796 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.796.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.796 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.796.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.797.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.797.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.797 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.797.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.797 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.797.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.797 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.797.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.797 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.797.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.797 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.797.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.797 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.797.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.797 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.797.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.797 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.797.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.797 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.797.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.797 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.797.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.798.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.798.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.798 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.798.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.798 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.798.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.798 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.798.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.798 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.798.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.798 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.798.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.798 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.798.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.798 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.798.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.798 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.798.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.798 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.798.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.798 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.798.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.799.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.799.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.799 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.799.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.799 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.799.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.799 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.799.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.799 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.799.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.799 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.799.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.799 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.799.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.799 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.799.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.799 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.799.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.799 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.799.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.799 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/79/PGA_scaffold34__164_contigs__length_87950420.799.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.800.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.800.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.800 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.800.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.800 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.800.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.800 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.800.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.800 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.800.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.800 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.800.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.800 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.800.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.800 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.800.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.800 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.800.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.800 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.800.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.800 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.800.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.801.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.801.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.801 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.801.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.801 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.801.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.801 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.801.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.801 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.801.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.801 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.801.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.801 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.801.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.801 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.801.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.801 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.801.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.801 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.801.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.801 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.801.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.802.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.802.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.802 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.802.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.802 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.802.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.802 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.802.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.802 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.802.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.802 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.802.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.802 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.802.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.802 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.802.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.802 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.802.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.802 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.802.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.802 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.802.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.803.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.803.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.803 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.803.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.803 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.803.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.803 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.803.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.803 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.803.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.803 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.803.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.803 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.803.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.803 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.803.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.803 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.803.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.803 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.803.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.803 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.803.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.804.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.804.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.804 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.804.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.804 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.804.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.804 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.804.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.804 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.804.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.804 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.804.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.804 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.804.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.804 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.804.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.804 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.804.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.804 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.804.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.804 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.804.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.805.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.805.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.805 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.805.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.805 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.805.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.805 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.805.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.805 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.805.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.805 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.805.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.805 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.805.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.805 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.805.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.805 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.805.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.805 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.805.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.805 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.805.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.806.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.806.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.806 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.806.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.806 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.806.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.806 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.806.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.806 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.806.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.806 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.806.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.806 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.806.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.806 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.806.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.806 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.806.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.806 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.806.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.806 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.806.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.807.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.807.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.807 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.807.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.807 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.807.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.807 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.807.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.807 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.807.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.807 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.807.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.807 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.807.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.807 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.807.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.807 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.807.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.807 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.807.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.807 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.807.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.808.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.808.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.808 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.808.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.808 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.808.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.808 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.808.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.808 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.808.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.808 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.808.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.808 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.808.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.808 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.808.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.808 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.808.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.808 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.808.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.808 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.808.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.809.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.809.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.809 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.809.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.809 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.809.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.809 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.809.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.809 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.809.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.809 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.809.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.809 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.809.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.809 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.809.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.809 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.809.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.809 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.809.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.809 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/80/PGA_scaffold34__164_contigs__length_87950420.809.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.810.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.810.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.810 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.810.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.810 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.810.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.810 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.810.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.810 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.810.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.810 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.810.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.810 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.810.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.810 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.810.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:5 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.810 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.810.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.810 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.810.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.810 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.810.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:3 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.811.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.811.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.811 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.811.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.811 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.811.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.811 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.811.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.811 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.811.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.811 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.811.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.811 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.811.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.811 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.811.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.811 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.811.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.811 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.811.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.811 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.811.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.812.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.812.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.812 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.812.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.812 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.812.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.812 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.812.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.812 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.812.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.812 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.812.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.812 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.812.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.812 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.812.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.812 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.812.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.812 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.812.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.812 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.812.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.813.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.813.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.813 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.813.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.813 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.813.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.813 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.813.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.813 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.813.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.813 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.813.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.813 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.813.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.813 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.813.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.813 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.813.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.813 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.813.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.813 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.813.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.814.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.814.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.814 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.814.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.814 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.814.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.814 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.814.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.814 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.814.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.814 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.814.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.814 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.814.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.814 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.814.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.814 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.814.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.814 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.814.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.814 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.814.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.815.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.815.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.815 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.815.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.815 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.815.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.815 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.815.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.815 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.815.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.815 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.815.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.815 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.815.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.815 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.815.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.815 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.815.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.815 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.815.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.815 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.815.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.816.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.816.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.816 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.816.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.816 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.816.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.816 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.816.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.816 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.816.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.816 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.816.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.816 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.816.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.816 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.816.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.816 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.816.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.816 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.816.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.816 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.816.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.817.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.817.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.817 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.817.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.817 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.817.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.817 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.817.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.817 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.817.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.817 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.817.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.817 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.817.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.817 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.817.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.817 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.817.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.817 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.817.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.817 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.817.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.818.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.818.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.818 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.818.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.818 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.818.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.818 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.818.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.818 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.818.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.818 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.818.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.818 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.818.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.818 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.818.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.818 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.818.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.818 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.818.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.818 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.818.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.819.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.819.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.819 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.819.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.819 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.819.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.819 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.819.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.819 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.819.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.819 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.819.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.819 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.819.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.819 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.819.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.819 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.819.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.819 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.819.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.819 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/81/PGA_scaffold34__164_contigs__length_87950420.819.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.820.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.820.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.820 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.820.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.820 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.820.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.820 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.820.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.820 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.820.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.820 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.820.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.820 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.820.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.820 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.820.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.820 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.820.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.820 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.820.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.820 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.820.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.821.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.821.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.821 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.821.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.821 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.821.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.821 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.821.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.821 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.821.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.821 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.821.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.821 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.821.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.821 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.821.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.821 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.821.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.821 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.821.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.821 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.821.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.822.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.822.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.822 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.822.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.822 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.822.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.822 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.822.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.822 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.822.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.822 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.822.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.822 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.822.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.822 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.822.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.822 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.822.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.822 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.822.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.822 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.822.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.823.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.823.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.823 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.823.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.823 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.823.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.823 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.823.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.823 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.823.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.823 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.823.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.823 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.823.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.823 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.823.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.823 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.823.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.823 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.823.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.823 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.823.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.824.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.824.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.824 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.824.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.824 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.824.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.824 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.824.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.824 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.824.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.824 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.824.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.824 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.824.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.824 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.824.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.824 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.824.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.824 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.824.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.824 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.824.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.825.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.825.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.825 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.825.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.825 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.825.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.825 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.825.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.825 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.825.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.825 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.825.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.825 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.825.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.825 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.825.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.825 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.825.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.825 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.825.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.825 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.825.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.826.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.826.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.826 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.826.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.826 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.826.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.826 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.826.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.826 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.826.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.826 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.826.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.826 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.826.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.826 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.826.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.826 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.826.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.826 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.826.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.826 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.826.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.827.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.827.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.827 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.827.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.827 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.827.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.827 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.827.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.827 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.827.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.827 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.827.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.827 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.827.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.827 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.827.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.827 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.827.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.827 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.827.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.827 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.827.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.828.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.828.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.828 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.828.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.828 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.828.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.828 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.828.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.828 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.828.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.828 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.828.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.828 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.828.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.828 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.828.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.828 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.828.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.828 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.828.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.828 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.828.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.829.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.829.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.829 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.829.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.829 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.829.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.829 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.829.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.829 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.829.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.829 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.829.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.829 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.829.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.829 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.829.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.829 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.829.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.829 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.829.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.829 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/82/PGA_scaffold34__164_contigs__length_87950420.829.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.830.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.830.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.830 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.830.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.830 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.830.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.830 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.830.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.830 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.830.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.830 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.830.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.830 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.830.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.830 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.830.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.830 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.830.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.830 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.830.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.830 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.830.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.831.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.831.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.831 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.831.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.831 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.831.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.831 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.831.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.831 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.831.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.831 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.831.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.831 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.831.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.831 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.831.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.831 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.831.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.831 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.831.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.831 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.831.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.832.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.832.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.832 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.832.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.832 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.832.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.832 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.832.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.832 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.832.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.832 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.832.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.832 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.832.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.832 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.832.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.832 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.832.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.832 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.832.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.832 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.832.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.833.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.833.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.833 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.833.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.833 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.833.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.833 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.833.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.833 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.833.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.833 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.833.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.833 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.833.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.833 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.833.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.833 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.833.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.833 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.833.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.833 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.833.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.834.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.834.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.834 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.834.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.834 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.834.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.834 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.834.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.834 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.834.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.834 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.834.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.834 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.834.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.834 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.834.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.834 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.834.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.834 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.834.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.834 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.834.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.835.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.835.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.835 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.835.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.835 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.835.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.835 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.835.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.835 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.835.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.835 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.835.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.835 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.835.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.835 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.835.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.835 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.835.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.835 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.835.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.835 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.835.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.836.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.836.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.836 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.836.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.836 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.836.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.836 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.836.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.836 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.836.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.836 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.836.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.836 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.836.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.836 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.836.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.836 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.836.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.836 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.836.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.836 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.836.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.837.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.837.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.837 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.837.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.837 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.837.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.837 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.837.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.837 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.837.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.837 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.837.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.837 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.837.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.837 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.837.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.837 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.837.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.837 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.837.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.837 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.837.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.838.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.838.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.838 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.838.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:34 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.838 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.838.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:25 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.838 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.838.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:21 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.838 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.838.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:19 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.838 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.838.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:26 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.838 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.838.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:31 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.838 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.838.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:27 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.838 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.838.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:33 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.838 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.838.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:28 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.838 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.838.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:35 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.839.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.839.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.839 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.839.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.839 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.839.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.839 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.839.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.839 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.839.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.839 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.839.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.839 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.839.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.839 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.839.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.839 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.839.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.839 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.839.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.839 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/83/PGA_scaffold34__164_contigs__length_87950420.839.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.840.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.840.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.840 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.840.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.840 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.840.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.840 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.840.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.840 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.840.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.840 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.840.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.840 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.840.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.840 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.840.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.840 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.840.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.840 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.840.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.840 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.840.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.841.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.841.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.841 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.841.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.841 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.841.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.841 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.841.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.841 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.841.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.841 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.841.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.841 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.841.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.841 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.841.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.841 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.841.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.841 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.841.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.841 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.841.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.842.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.842.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.842 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.842.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.842 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.842.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.842 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.842.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.842 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.842.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.842 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.842.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.842 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.842.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.842 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.842.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.842 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.842.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.842 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.842.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.842 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.842.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.843.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.843.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.843 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.843.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.843 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.843.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.843 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.843.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.843 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.843.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.843 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.843.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.843 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.843.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:6 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.843 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.843.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.843 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.843.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.843 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.843.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:8 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.843 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.843.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:4 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.844.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.844.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.844 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.844.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.844 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.844.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.844 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.844.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.844 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.844.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.844 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.844.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.844 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.844.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.844 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.844.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.844 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.844.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.844 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.844.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.844 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.844.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.845.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.845.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.845 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.845.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.845 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.845.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.845 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.845.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.845 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.845.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.845 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.845.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.845 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.845.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.845 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.845.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.845 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.845.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.845 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.845.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.845 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.845.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.846.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.846.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.846 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.846.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.846 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.846.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.846 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.846.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.846 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.846.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.846 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.846.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.846 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.846.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.846 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.846.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.846 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.846.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.846 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.846.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.846 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.846.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.847.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.847.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.847 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.847.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.847 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.847.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.847 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.847.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.847 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.847.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.847 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.847.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.847 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.847.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.847 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.847.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.847 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.847.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.847 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.847.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.847 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.847.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.848.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.848.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.848 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.848.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.848 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.848.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.848 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.848.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.848 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.848.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.848 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.848.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.848 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.848.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.848 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.848.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.848 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.848.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.848 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.848.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.848 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.848.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.849.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.849.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.849 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.849.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.849 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.849.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.849 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.849.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.849 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.849.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.849 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.849.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.849 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.849.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.849 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.849.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.849 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.849.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.849 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.849.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.849 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/84/PGA_scaffold34__164_contigs__length_87950420.849.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.850.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.850.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.850 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.850.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.850 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.850.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.850 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.850.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.850 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.850.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.850 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.850.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.850 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.850.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.850 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.850.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.850 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.850.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.850 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.850.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.850 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.850.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.851.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.851.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.851 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.851.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.851 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.851.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.851 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.851.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.851 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.851.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.851 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.851.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.851 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.851.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.851 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.851.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.851 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.851.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.851 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.851.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.851 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.851.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.852.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.852.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.852 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.852.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.852 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.852.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.852 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.852.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.852 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.852.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.852 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.852.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.852 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.852.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.852 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.852.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.852 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.852.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.852 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.852.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.852 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.852.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:1 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.853.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.853.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.853 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.853.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.853 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.853.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.853 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.853.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.853 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.853.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.853 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.853.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.853 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.853.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.853 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.853.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.853 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.853.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.853 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.853.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.853 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.853.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.854.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.854.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.854 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.854.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.854 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.854.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.854 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.854.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.854 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.854.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.854 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.854.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.854 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.854.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.854 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.854.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.854 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.854.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.854 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.854.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.854 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.854.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.855.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.855.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.855 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.855.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.855 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.855.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.855 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.855.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.855 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.855.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.855 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.855.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.855 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.855.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.855 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.855.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.855 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.855.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.855 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.855.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.855 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.855.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.856.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.856.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.856 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.856.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.856 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.856.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.856 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.856.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.856 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.856.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.856 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.856.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.856 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.856.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.856 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.856.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.856 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.856.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.856 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.856.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.856 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.856.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.857.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.857.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.857 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.857.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.857 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.857.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.857 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.857.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.857 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.857.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.857 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.857.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.857 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.857.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.857 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.857.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.857 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.857.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.857 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.857.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.857 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.857.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.858.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.858.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.858 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.858.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.858 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.858.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.858 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.858.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.858 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.858.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.858 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.858.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.858 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.858.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.858 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.858.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.858 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.858.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.858 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.858.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.858 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.858.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.859.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.859.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.859 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.859.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.859 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.859.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.859 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.859.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.859 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.859.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.859 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.859.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.859 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.859.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.859 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.859.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.859 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.859.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.859 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.859.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.859 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/85/PGA_scaffold34__164_contigs__length_87950420.859.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.860.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.860.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.860 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.860.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.860 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.860.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.860 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.860.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.860 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.860.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.860 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.860.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.860 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.860.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.860 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.860.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.860 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.860.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.860 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.860.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.860 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.860.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.861.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.861.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.861 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.861.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.861 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.861.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.861 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.861.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.861 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.861.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.861 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.861.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.861 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.861.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.861 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.861.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.861 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.861.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.861 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.861.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.861 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.861.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.862.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.862.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.862 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.862.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.862 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.862.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.862 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.862.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.862 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.862.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.862 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.862.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.862 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.862.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.862 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.862.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.862 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.862.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.862 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.862.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.862 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.862.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
Warning: [blastx] Query_1 PGA_scaffold34__1.. : Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.863.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.863.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.863 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.863.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:3 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.863 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.863.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.863 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.863.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.863 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.863.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.863 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.863.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.863 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.863.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.863 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.863.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.863 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.863.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.863 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.863.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:4 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.863 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.863.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:2 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.864.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.864.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.864 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.864.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.864 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.864.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.864 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.864.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.864 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.864.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.864 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.864.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.864 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.864.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.864 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.864.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.864 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.864.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.864 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.864.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.864 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.864.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.865.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.865.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.865 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.865.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.865 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.865.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.865 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.865.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.865 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.865.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.865 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.865.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.865 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.865.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.865 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.865.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.865 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.865.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.865 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.865.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.865 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.865.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.866.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.866.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.866 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.866.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.866 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.866.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.866 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.866.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.866 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.866.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.866 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.866.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.866 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.866.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.866 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.866.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.866 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.866.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.866 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.866.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.866 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.866.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.867.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.867.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.867 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.867.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.867 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.867.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.867 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.867.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.867 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.867.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.867 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.867.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.867 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.867.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.867 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.867.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.867 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.867.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.867 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.867.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.867 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.867.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.868.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.868.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.868 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.868.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.868 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.868.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.868 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.868.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.868 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.868.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.868 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.868.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.868 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.868.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.868 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.868.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.868 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.868.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.868 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.868.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.868 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.868.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.869.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.869.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.869 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.869.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.869 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.869.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.869 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.869.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.869 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.869.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.869 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.869.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.869 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.869.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.869 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.869.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.869 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.869.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.869 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.869.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.869 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/86/PGA_scaffold34__164_contigs__length_87950420.869.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.870.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.870.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.870 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.870.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.870 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.870.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.870 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.870.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.870 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.870.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.870 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.870.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.870 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.870.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.870 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.870.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.870 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.870.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.870 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.870.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.870 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.870.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.871.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.871.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.871 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.871.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.871 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.871.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.871 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.871.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.871 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.871.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.871 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.871.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.871 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.871.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.871 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.871.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.871 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.871.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.871 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.871.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.871 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.871.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.872.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.872.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.872 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.872.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.872 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.872.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.872 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.872.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.872 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.872.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.872 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.872.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.872 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.872.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.872 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.872.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.872 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.872.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.872 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.872.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.872 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.872.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.873.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.873.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.873 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.873.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.873 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.873.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.873 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.873.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.873 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.873.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.873 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.873.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.873 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.873.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.873 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.873.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.873 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.873.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.873 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.873.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.873 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.873.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.874.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.874.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.874 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.874.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.874 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.874.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.874 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.874.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.874 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.874.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.874 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.874.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.874 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.874.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.874 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.874.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.874 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.874.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.874 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.874.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.874 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.874.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.875.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.875.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.875 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.875.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.875 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.875.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.875 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.875.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.875 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.875.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.875 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.875.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.875 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.875.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.875 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.875.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.875 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.875.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.875 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.875.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.875 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.875.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.876.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.876.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.876 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.876.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.876 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.876.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.876 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.876.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.876 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.876.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.876 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.876.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.876 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.876.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.876 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.876.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.876 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.876.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.876 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.876.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.876 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.876.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.877.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.877.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.877 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.877.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.877 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.877.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.877 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.877.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.877 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.877.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.877 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.877.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.877 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.877.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.877 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.877.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.877 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.877.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.877 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.877.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.877 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.877.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.878.all.rb -species all -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87 -pa 1
#-------------------------------#
running repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_nNIkWB; /home/ec2-user/MAKERTOOLS/maker/exe/RepeatMasker/RepeatMasker /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.878.evans_trout_hap2%2Efasta-families%2Efa.specific -dir /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87 -pa 1 -lib /home/ec2-user/PGScratch/evans_trout_hap2.fasta-families.fa
#-------------------------------#
Warning...unknown stuff <
>
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.878 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.878.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.878 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.878.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.878 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.878.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.878 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.878.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.878 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.878.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.878 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.878.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.878 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.878.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:1 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.878 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.878.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.878 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.878.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:2 hits
doing blastx repeats
running blast search.
#--------- command -------------#
Widget::blastx:
/usr/local/bin/blastx -db /tmp/maker_nNIkWB/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_nNIkWB/0/PGA_scaffold34__164_contigs__length_87950420.878 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 1 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ec2-user/PGScratch/scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/87/PGA_scaffold34__164_contigs__length_87950420.878.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:2 hits
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
preparing masked sequence
preparing ab-inits
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ec2-user/MAKERTOOLS/maker/exe/augustus/bin/augustus --species=BUSCO_evans_trout_hap1 --UTR=off /tmp/maker_nNIkWB/PGA_scaffold34__164_contigs__length_87950420.abinit_masked.0 > /tmp/maker_nNIkWB/PGA_scaffold34__164_contigs__length_87950420.abinit_masked.0.BUSCO_evans_trout_hap1.augustus
#-------------------------------#
Could not find the config file /home/ec2-user/MAKERTOOLS/maker/exe/augustus/config/species/BUSCO_evans_trout_hap1/BUSCO_evans_trout_hap1_parameters.cfg.
Looking for BUSCO_evans_trout_hap1_parameters.cfg in the configuration directory instead ... not found.
/home/ec2-user/MAKERTOOLS/maker/exe/augustus/bin/augustus: ERROR
Species-specific configuration files not found in /home/ec2-user/MAKERTOOLS/maker/exe/augustus/config/species/. Type "augustus --species=help" to see available species.
Could not find the config file /home/ec2-user/MAKERTOOLS/maker/exe/augustus/config/species/BUSCO_evans_trout_hap1/BUSCO_evans_trout_hap1_parameters.cfg.
Looking for BUSCO_evans_trout_hap1_parameters.cfg in the configuration directory instead ... not found.
/home/ec2-user/MAKERTOOLS/maker/exe/augustus/bin/augustus: ERROR
Species-specific configuration files not found in /home/ec2-user/MAKERTOOLS/maker/exe/augustus/config/species/. Type "augustus --species=help" to see available species.
ERROR: Augustus failed
--> rank=NA, hostname=ip-172-31-50-142
ERROR: Failed while preparing ab-inits
ERROR: Chunk failed at level:0, tier_type:2
FAILED CONTIG:PGA_scaffold34__164_contigs__length_87950420
ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:PGA_scaffold34__164_contigs__length_87950420
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/PGA_scaffold34__164_contigs__length_87950420.abinit_masked.0.BUSCO_evans_trout_hap1.augustus
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: PGA_scaffold34__164_contigs__length_87950420
Length: 87950420
Tries: 2!!
#---------------------------------------------------------------------
setting up GFF3 output and fasta chunks
preparing ab-inits
running augustus.
#--------- command -------------#
Widget::augustus:
/home/ec2-user/MAKERTOOLS/maker/exe/augustus/bin/augustus --species=BUSCO_evans_trout_hap1 --UTR=off /tmp/maker_nNIkWB/PGA_scaffold34__164_contigs__length_87950420.abinit_masked.0 > /tmp/maker_nNIkWB/PGA_scaffold34__164_contigs__length_87950420.abinit_masked.0.BUSCO_evans_trout_hap1.augustus
#-------------------------------#
Could not find the config file /home/ec2-user/MAKERTOOLS/maker/exe/augustus/config/species/BUSCO_evans_trout_hap1/BUSCO_evans_trout_hap1_parameters.cfg.
Looking for BUSCO_evans_trout_hap1_parameters.cfg in the configuration directory instead ... not found.
/home/ec2-user/MAKERTOOLS/maker/exe/augustus/bin/augustus: ERROR
Species-specific configuration files not found in /home/ec2-user/MAKERTOOLS/maker/exe/augustus/config/species/. Type "augustus --species=help" to see available species.
Could not find the config file /home/ec2-user/MAKERTOOLS/maker/exe/augustus/config/species/BUSCO_evans_trout_hap1/BUSCO_evans_trout_hap1_parameters.cfg.
Looking for BUSCO_evans_trout_hap1_parameters.cfg in the configuration directory instead ... not found.
/home/ec2-user/MAKERTOOLS/maker/exe/augustus/bin/augustus: ERROR
Species-specific configuration files not found in /home/ec2-user/MAKERTOOLS/maker/exe/augustus/config/species/. Type "augustus --species=help" to see available species.
ERROR: Augustus failed
--> rank=NA, hostname=ip-172-31-50-142
ERROR: Failed while preparing ab-inits
ERROR: Chunk failed at level:0, tier_type:2
FAILED CONTIG:PGA_scaffold34__164_contigs__length_87950420
ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:PGA_scaffold34__164_contigs__length_87950420
examining contents of the fasta file and run log
--Next Contig--
Processing run.log file...
MAKER WARNING: The file scaffold34.maker.output/scaffold34_datastore/9D/2C/PGA_scaffold34__164_contigs__length_87950420//theVoid.PGA_scaffold34__164_contigs__length_87950420/PGA_scaffold34__164_contigs__length_87950420.abinit_masked.0.BUSCO_evans_trout_hap1.augustus
did not finish on the last run and must be erased
Maker is now finished!!!
Start_time: 1691702316
End_time: 1691741802
Elapsed: 39486
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