BRAKER gene prediction pipeline with RNA-seq data.
>contig_26
TTTGATTTAGTTTATCAAATACCTTATACTAAACCTGATATGTAATATAACCCCCTGAAATACCAATTTATCAAAACAGTTAAAATCTTTTAATGTTTTAGTAAAACTACCAGACTTTCTGGCACTACTCCTGTCTGATCTCATTGAACTTCTGTCTTTCTTTCCCATCTCTCTACTTGATCTGTTACTATTGGATTGTGCACTAGCTCGTTGCCTCAATTTGATATTATGGTTATCTTTCTCCTCCTCTACCATAACAATATCAATTTATCACACACTTTCCTTCTACTCGCTCTTAGAGTCACTCTCTATGATTTGTCTGAACAGAGGTATTCTCTTGGCCTCCTTTAGAAATAGCTCTCCGTGGTTAAAGTACAATGAAATTGTATCCCAACCTTCGGATCATCCTGAGCCCAGAGTAACTATTTTTGTTGCATTTTCACAGTGCTATTTTTGTCGATGTTATAGTTGGAAATGTATTTCCGTCCTGCTCTTGTTTTTTCTGTTCTTTCCACAACTTTTTTTAGACTCTAAACCAAAATAAATTGTGATAATCTTTTCTTTTGGGATAAATATTATCGGTTCTGATTTGTTGCCTTAAAATTTAATATGGTTCCCTTTAAAGTAGTTTATTTATATTTTTTTTTTGTATTTTGATTTGATTTTTTTTGGAAATTCAATATTTTGGAGAAAAATAATTTAAAATCTTTTGTCTCTCAATTTTGAAGATTTTCATAAATTTTCTGACTATAAATTTATAAAATTTACTTTACAGTTGTATTTGTAAACAAAATAAATGTTTTTAAGAATATTTATATTCATTTGAAAATATCAAATCAATTAAATTCTAGTAATTTAATACTTTTTTCAACTGAATGAAAAAAAATTGTTAAAAATTTATAATTCTATAATTTTTAACCTATAAACATTGACACACTTAACACTAACTGTTTTACCTTTGATTTTCAAAGTGCATTTATCATGCAAATTACTTTGTTCGGGGAAGTGTTAAGAAATATTGGCCATTCACGGCACAAATTAGAGGCATGACAGTGGATGAAGCAGAAACACAACTGAAATTCCAGCAAAAGTCTTTTGCTCACACCATAAAACAACTTATTACAGAGGCAGCTGATCTGGCAGTTAAAGATTACAATGTGGAATTTAGATCCGAGCTGTGGATAGGTAACACTTAAAACTTACCTCTTTAAAATGTTAGAGAGAATGTTTGTGACCAAAGCAGGTAGTTTGAAAGGTCTGAGGAAAATGAGATTGAATATTGTGTGTCCCAAAACAAGATATAGTCATTTGTTTGTAAAACTTACCGAAGGCAATAAACCTGAAAATTATTATGAGGTTGAGCCAACTAGATACGAATTGGCAGAAAAATACTTTGACAAACTTTACAGAAGAAGAATTGAGGAAGGTTTATAAAATTGTATTGATAATTGAATATATTTACATTTTCATTATAATATAATACTTCGAAAGTGGATAATAGAATATTCCTAAAATTGAATATCAAACCACAAATTTAATCAACAAATATTAAATACTTTGTTTGTTTGTTTTATTCCATGGATAAATAGAGGATTTTTCTTAGAATTATTTATAGAAATATTTTTATTTTAAATAATATAATTTATATCAAATTACCGAAATATTGAAAGATACAAAGTTTATTTCATTATTTTCTTTTAAAAATTATTTCATTCAGTTTTGCTTTAAACAGAAATAACTTTTCAAAATCTACATTTATCACAATTTACCTCTTCTATCCTTACACATGAGACATGTCAAACTTAAAAATAGTTCATTGTTGTACATTTTAAAAAATTATAAATTTTTTTGTTTAAAATAAATATTTCTGAGGTTTAACTTCATAGAAAATAATAAGTTGATCAGGAAAGAAATATTTGGATCATCAAATAGAGGACCATAAAGGAAATTATTATTCCTTCCAGACATCATAATAGACCACCCTATATCCTATGTTCAAATTTACTTCATCTATGATCTTGGGACTGTCGGGAGTTGTAAATATTTATAAGATTTCCTTCACTGCTTTGTATATAATTTATTTGTATAATTTTATGTATATCAATTATTATTTTTAAGTAAAACAGTTAGGATTTAGTTTATAGAGAGAACTGGGAGGCGTTGGACAAAAAGGAGAAGTGAAAAGGAAATAGAAATATTCCTCATGAACTTAAGTCCTTGATCCTGTTATTGTAGAGTCTCATTAAACATGAAATTTGAATAAAGACATATTTGATCGAAAAGATAGAGCTGGAAATATTTTAAGGACCAAAATAACTAAACTCCAGTGCTAAACCTTTTTTTGGATGAATTGATTTAAAAAGATAATTCTAATCCCATTCACTTAGATTCAACAAAAATCCTTAAGACCAAAGATTTTTTGGCTCCAAGGACTTTTACGAAGAGAAGAGATAAAAAGAAAAAAATTCTAAATCTAAAAATTGGGAACAGAAGAGACTTTTCAAAAAGTAGAACGATTCAGCACTAAATGGATGATACTGTCCCTAACTCTTCGGTACAAAATGGTTTCTAAAATACAAAATTCAGAGACGAGGCACAAAAACTTCTATGTAAAAAAAAATATTTTGTAGTTGAATTAAATTTGGACACTTATTCCCCATGCCTGATCATTTTGGGTCTCGTTCCAATGAGGTGAAGGAGGAGGTGGTGCGGTTGGCTATAGTGAAGCCTGACCTGTGCAAACCAAACAAATGCAAGGGAGAGTGTGCTGCTATATGTCCTGTGAACAGGAGTAGGCCAGGAAATCTTATGAGCACTGGAAACAGTGGAGGTATATCTAGAAAATTATATATTTTTTGTTGCTTTTATTTTAAATTTGTGCGAGTGTTGGGGAACTGATGGGGTATCTAAAAATGATTTTCCTTAATCAAATTGAATGTATTCATGTATCTGTAGGTTTGGCTAAAAAATTATGACCATAAGTAAACAA>contig_26
TTTGATTTAGTTTATCAAATACCTTATACTAAACCTGATATGTAATATAACCCCCTGAAATACCAATTTATCAAAACAGTTAAAATCTTTTAATGTTTTAGTAAAACTACCAGACTTTCTGGCACTACTCCTGTCTGATCTCATTGAACTTCTGTCTTTCTTTCCCATCTCTCTACTTGATCTGTTACTATTGGATTGTGCACTAGCTCGTTGCCTCAATTTGATATTATGGTTATCTTTCTCCTCCTCTACCATAACAATATCAATTTATCACACACTTTCCTTCTACTCGCTCTTAGAGTCACTCTCTATGATTTGTCTGAACAGAGGTATTCTCTTGGCCTCCTTTAGAAATAGCTCTCCGTGGTTAAAGTACAATGAAATTGTATCCCAACCTTCGGATCATCCTGAGCCCAGAGTAACTATTTTTGTTGCATTTTCACAGTGCTATTTTTGTCGATGTTATAGTTGGAAATGTATTTCCGTCCTGCTCTTGTTTTTTCTGTTCTTTCCACAACTTTTTTTAGACTCTAAACCAAAATAAATTGTGATAATCTTTTCTTTTGGGATAAATATTATCGGTTCTGATTTGTTGCCTTAAAATTTAATATGGTTCCCTTTAAAGTAGTTTATTTATATTTTTTTTTTGTATTTTGATTTGATTTTTTTTGGAAATTCAATATTTTGGAGAAAAATAATTTAAAATCTTTTGTCTCTCAATTTTGAAGATTTTCATAAATTTTCTGACTATAAATTTATAAAATTTACTTTACAGTTGTATTTGTAAACAAAATAAATGTTTTTAAGAATATTTATATTCATTTGAAAATATCAAATCAATTAAATTCTAGTAATTTAATACTTTTTTCAACTGAATGAAAAAAAATTGTTAAAAATTTATAATTCTATAATTTTTAACCTATAAACATTGACACACTTAACACTAACTGTTTTACCTTTGATTTTCAAAGTGCATTTATCATGCAAATTACTTTGTTCGGGGAAGTGTTAAGAAATATTGGCCATTCACGGCACAAATTAGAGGCATGACAGTGGATGAAGCAGAAACACAACTGAAATTCCAGCAAAAGTCTTTTGCTCACACCATAAAACAACTTATTACAGAGGCAGCTGATCTGGCAGTTAAAGATTACAATGTGGAATTTAGATCCGAGCTGTGGATAGGTAACACTTAAAACTTACCTCTTTAAAATGTTAGAGAGAATGTTTGTGACCAAAGCAGGTAGTTTGAAAGGTCTGAGGAAAATGAGATTGAATATTGTGTGTCCCAAAACAAGATATAGTCATTTGTTTGTAAAACTTACCGAAGGCAATAAACCTGAAAATTATTATGAGGTTGAGCCAACTAGATACGAATTGGCAGAAAAATACTTTGACAAACTTTACAGAAGAAGAATTGAGGAAGGTTTATAAAATTGTATTGATAATTGAATATATTTACATTTTCATTATAATATAATACTTCGAAAGTGGATAATAGAATATTCCTAAAATTGAATATCAAACCACAAATTTAATCAACAAATATTAAATACTTTGTTTGTTTGTTTTATTCCATGGATAAATAGAGGATTTTTCTTAGAATTATTTATAGAAATATTTTTATTTTAAATAATATAATTTATATCAAATTACCGAAATATTGAAAGATACAAAGTTTATTTCATTATTTTCTTTTAAAAATTATTTCATTCAGTTTTGCTTTAAACAGAAATAACTTTTCAAAATCTACATTTATCACAATTTACCTCTTCTATCCTTACACATGAGACATGTCAAACTTAAAAATAGTTCATTGTTGTACATTTTAAAAAATTATAAATTTTTTTGTTTAAAATAAATATTTCTGAGGTTTAACTTCATAGAAAATAATAAGTTGATCAGGAAAGAAATATTTGGATCATCAAATAGAGGACCATAAAGGAAATTATTATTCCTTCCAGACATCATAATAGACCACCCTATATCCTATGTTCAAATTTACTTCATCTATGATCTTGGGACTGTCGGGAGTTGTAAATATTTATAAGATTTCCTTCACTGCTTTGTATATAATTTATTTGTATAATTTTATGTATATCAATTATTATTTTTAAGTAAAACAGTTAGGATTTAGTTTATAGAGAGAACTGGGAGGCGTTGGACAAAAAGGAGAAGTGAAAAGGAAATAGAAATATTCCTCATGAACTTAAGTCCTTGATCCTGTTATTGTAGAGTCTCATTAAACATGAAATTTGAATAAAGACATATTTGATCGAAAAGATAGAGCTGGAAATATTTTAAGGACCAAAATAACTAAACTCCAGTGCTAAACCTTTTTTTGGATGAATTGATTTAAAAAGATAATTCTAATCCCATTCACTTAGATTCAACAAAAATCCTTAAGACCAAAGATTTTTTGGCTCCAAGGACTTTTACGAAGAGAAGAGATAAAAAGAAAAAAATTCTAAATCTAAAAATTGGGAACAGAAGAGACTTTTCAAAAAGTAGAACGATTCAGCACTAAATGGATGATACTGTCCCTAACTCTTCGGTACAAAATGGTTTCTAAAATACAAAATTCAGAGACGAGGCACAAAAACTTCTATGTAAAAAAAAATATTTTGTAGTTGAATTAAATTTGGACACTTATTCCCCATGCCTGATCATTTTGGGTCTCGTTCCAATGAGGTGAAGGAGGAGGTGGTGCGGTTGGCTATAGTGAAGCCTGACCTGTGCAAACCAAACAAATGCAAGGGAGAGTGTGCTGCTATATGTCCTGTGAACAGGAGTAGGCCAGGAAATCTTATGAGCACTGGAAACAGTGGAGGTATATCTAGAAAATTATATATTTTTTGTTGCTTTTATTTTAAATTTGTGCGAGTGTTGGGGAACTGATGGGGTATCTAAAAATGATTTTCCTTAATCAAATTGAATGTATTCATGTATCTGTAGGTTTGGCTAAAAAATTATGACCATAAGTAAACAAannotation~BRAKER3 -c 8 -m 32 input_1/ input_2/parasite.fa
contig_10054 AUGUSTUS gene 3165 9627 . - . g1___evalue-
contig_10054 AUGUSTUS transcript 3165 9627 0.63 - . g1.t1_BRM_DROME_BRM_DROME_ATP-dependent_helicase_brm_evalue-0.0
contig_10054 AUGUSTUS stop_codon 3165 3167 . - 0 transcript_id "g1.t1_BRM_DROME_BRM_DROME_ATP-dependent_helicase_brm_evalue-0.0"; gene_id "g1";
contig_10054 AUGUSTUS CDS 3165 3230 1 - 0 transcript_id "g1.t1_BRM_DROME_BRM_DROME_ATP-dependent_helicase_brm_evalue-0.0"; gene_id "g1";
contig_10054 AUGUSTUS exon 3165 3230 . - . transcript_id "g1.t1_BRM_DROME_BRM_DROME_ATP-dependent_helicase_brm_evalue-0.0"; gene_id "g1";
contig_10054 AUGUSTUS intron 3231 3269 1 - . transcript_id "g1.t1_BRM_DROME_BRM_DROME_ATP-dependent_helicase_brm_evalue-0.0"; gene_id "g1";
contig_10054 AUGUSTUS CDS 3270 3589 1 - 2 transcript_id "g1.t1_BRM_DROME_BRM_DROME_ATP-dependent_helicase_brm_evalue-0.0"; gene_id "g1";
contig_10054 AUGUSTUS exon 3270 3589 . - . transcript_id "g1.t1_BRM_DROME_BRM_DROME_ATP-dependent_helicase_brm_evalue-0.0"; gene_id "g1";
contig_10054 AUGUSTUS intron 3590 3626 0.86 - . transcript_id "g1.t1_BRM_DROME_BRM_DROME_ATP-dependent_helicase_brm_evalue-0.0"; gene_id "g1";
contig_10054 AUGUSTUS CDS 3627 4161 0.86 - 0 transcript_id "g1.t1_BRM_DROME_BRM_DROME_ATP-dependent_helicase_brm_evalue-0.0"; gene_id "g1";
pp annotation~BRAKER3 -c 8 -m 32 input_1/ input_2/parasite.fa
Checking the realpath of input files.
0 input_1/
1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/input_1/S_l1_1.fq.gz
1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/input_1/S_l1_2.fq.gz
0 input_2/parasite.fa
0
0
/home/yoshitake.kazutoshi/work -> /data/yoshitake.kazutoshi/work
/home/yoshitake.kazutoshi/work/pp-dev -> /data/yoshitake.kazutoshi/work/pp-dev
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3
/data/yoshitake.kazutoshi/work
/data/yoshitake.kazutoshi/work/pp-dev
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3
biocontainers/emboss:v6.6.0dfsg-7b1-deb_cv1 c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 c2997108/ubuntu-18:braker2_hisat2_5 centos:centos6 quay.io/biocontainers/gffread:0.12.7--h9a82719_0 quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 quay.io/biocontainers/prinseq:0.20.4 quay.io/biocontainers/samtools:1.9--h10a08f8_12 quay.io/biocontainers/seqkit:0.12.1--0
using docker
++ docker pull biocontainers/emboss:v6.6.0dfsg-7b1-deb_cv1
v6.6.0dfsg-7b1-deb_cv1: Pulling from biocontainers/emboss
478cd0aa93c0: Pulling fs layer
94d6a239eb0e: Pulling fs layer
e8e87313e9cb: Pulling fs layer
1badce2e48be: Pulling fs layer
732b6ad56c57: Pulling fs layer
f464fdba1cc8: Pulling fs layer
f8a34b82a572: Pulling fs layer
1badce2e48be: Waiting
732b6ad56c57: Waiting
f8a34b82a572: Waiting
f464fdba1cc8: Waiting
94d6a239eb0e: Download complete
e8e87313e9cb: Download complete
478cd0aa93c0: Download complete
Checking the realpath of input files.
0 input_1/
1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/input_1/S_l1_1.fq.gz
1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/input_1/S_l1_2.fq.gz
0 input_2/parasite.fa
0
0
/home/yoshitake.kazutoshi/work -> /data/yoshitake.kazutoshi/work
/home/yoshitake.kazutoshi/work/pp-dev -> /data/yoshitake.kazutoshi/work/pp-dev
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3
/data/yoshitake.kazutoshi/work
/data/yoshitake.kazutoshi/work/pp-dev
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3
biocontainers/emboss:v6.6.0dfsg-7b1-deb_cv1 c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 c2997108/ubuntu-18:braker2_hisat2_5 centos:centos6 quay.io/biocontainers/gffread:0.12.7--h9a82719_0 quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 quay.io/biocontainers/prinseq:0.20.4 quay.io/biocontainers/samtools:1.9--h10a08f8_12 quay.io/biocontainers/seqkit:0.12.1--0
using docker
++ docker pull biocontainers/emboss:v6.6.0dfsg-7b1-deb_cv1
v6.6.0dfsg-7b1-deb_cv1: Pulling from biocontainers/emboss
478cd0aa93c0: Pulling fs layer
94d6a239eb0e: Pulling fs layer
e8e87313e9cb: Pulling fs layer
1badce2e48be: Pulling fs layer
732b6ad56c57: Pulling fs layer
f464fdba1cc8: Pulling fs layer
f8a34b82a572: Pulling fs layer
1badce2e48be: Waiting
732b6ad56c57: Waiting
f8a34b82a572: Waiting
f464fdba1cc8: Waiting
Checking the realpath of input files.
0 input_1/
1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/input_1/S_l1_1.fq.gz
1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/input_1/S_l1_2.fq.gz
0 input_2/parasite.fa
0
0
/home/yoshitake.kazutoshi/work -> /data/yoshitake.kazutoshi/work
/home/yoshitake.kazutoshi/work/pp-dev -> /data/yoshitake.kazutoshi/work/pp-dev
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3
/data/yoshitake.kazutoshi/work
/data/yoshitake.kazutoshi/work/pp-dev
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3
biocontainers/emboss:v6.6.0dfsg-7b1-deb_cv1 c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 c2997108/ubuntu-18:braker2_hisat2_5 centos:centos6 quay.io/biocontainers/gffread:0.12.7--h9a82719_0 quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 quay.io/biocontainers/prinseq:0.20.4 quay.io/biocontainers/samtools:1.9--h10a08f8_12 quay.io/biocontainers/seqkit:0.12.1--0
using podman
++ podman pull centos:centos6
Resolved "centos" as an alias (/etc/containers/registries.conf.d/000-shortnames.conf)
Trying to pull quay.io/centos/centos:centos6...
Getting image source signatures
Copying blob sha256:ff50d722b38227ec8f2bbf0cdbce428b66745077c173d8117d91376128fa532e
Copying config sha256:d0957ffdf8a2ea8c8925903862b65a1b6850dbb019f88d45e927d3d5a3fa0c31
Writing manifest to image destination
Storing signatures
d0957ffdf8a2ea8c8925903862b65a1b6850dbb019f88d45e927d3d5a3fa0c31
++ set +ex
+ set -o pipefail
++ find input_1//
++ egrep '(_R1.*|_1)[.]f(ast|)q$'
++ echo ''
+ r1=
++ find input_1//
++ egrep '(_R1.*|_1)[.]f(ast|)q[.]gz$'
+ r1gz=input_1//S_l1_1.fq.gz
+ '[' input_1//S_l1_1.fq.gz = '' ']'
+ r2=
++ for i in $r1gz
+++ echo input_1//S_l1_1.fq.gz
+++ egrep '_1[.]f(ast|)q[.]gz$'
+++ wc -l
++ '[' 1 = 1 ']'
++ echo input_1//S_l1_1.fq.gz
++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/'
+ r2gz=input_1//S_l1_2.fq.gz
+ echo '#Check paired-end'
#Check paired-end
+ ls input_1//S_l1_2.fq.gz
++ echo input_2/parasite.fa
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
+ awk '{if($0~"^>"){sub(/ .*/,"",$0)}; print $0}' input_2/parasite.fa
+ sed 's/\r//'
+ input_2=input_2/parasite.fa.ref.fa
++ basename ''
++ basename ''
+ '[' '!=' gmes_linux_64.tar.gz -o '!=' gm_key_64.gz ']'
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/annotation~BRAKER3: 64 行: [: 引数が多すぎます
+ FUNC_RUN_PODMAN quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 hisat2-build -p 8 input_2/parasite.fa.ref.fa hisat2_index
+ PP_RUN_IMAGE=quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20231113_200501_353_7108
+ echo pp20231113_200501_353_7108
++ echo quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4
++ awk -F/ '{if(NF==2){$0="docker.io/"$0}; print $0}'
+ PP_RUN_IMAGE=quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4
+ podman run --name pp20231113_200501_353_7108 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -i --rm quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 hisat2-build -p 8 input_2/parasite.fa.ref.fa hisat2_index
Settings:
Output files: "hisat2_index.*.ht2"
Line rate: 6 (line is 64 bytes)
Lines per side: 1 (side is 64 bytes)
Offset rate: 4 (one in 16)
FTable chars: 10
Strings: unpacked
Local offset rate: 3 (one in 8)
Local fTable chars: 6
Local sequence length: 57344
Local sequence overlap between two consecutive indexes: 1024
Endianness: little
Actual local endianness: little
Sanity checking: disabled
Assertions: disabled
Random seed: 0
Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
input_2/parasite.fa.ref.fa
Reading reference sizes
Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:00
Time to read SNPs and splice sites: 00:00:00
Using parameters --bmax 317396 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 317396 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:00:00
Allocating rank array
Ranking v-sort output
Ranking v-sort output time: 00:00:00
Invoking Larsson-Sadakane on ranks
Invoking Larsson-Sadakane on ranks time: 00:00:00
Sanity-checking and returning
Building samples
Reserving space for 86 sample suffixes
Generating random suffixes
QSorting 86 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 86 samples
(Using difference cover)
Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
Splitting and merging time: 00:00:00
Split 12, merged 39; iterating...
Splitting and merging
Splitting and merging time: 00:00:00
Split 7, merged 4; iterating...
Splitting and merging
Splitting and merging time: 00:00:00
Split 1, merged 4; iterating...
Splitting and merging
Splitting and merging time: 00:00:00
Avg bucket size: 229528 (target: 317395)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering GFM loop
Getting block 1 of 59
Reserving size (317396) for bucket 1
Getting block 2 of 59
Reserving size (317396) for bucket 2
Getting block 3 of 59
Reserving size (317396) for bucket 3
Calculating Z arrays for bucket 1
Getting block 4 of 59
Reserving size (317396) for bucket 4
Calculating Z arrays for bucket 3
Calculating Z arrays for bucket 2
Entering block accumulator loop for bucket 1:
Getting block 5 of 59
Reserving size (317396) for bucket 5
Calculating Z arrays for bucket 4
Calculating Z arrays for bucket 5
Entering block accumulator loop for bucket 3:
Entering block accumulator loop for bucket 2:
Entering block accumulator loop for bucket 5:
Entering block accumulator loop for bucket 4:
Getting block 6 of 59
Reserving size (317396) for bucket 6
Calculating Z arrays for bucket 6
Entering block accumulator loop for bucket 6:
Getting block 7 of 59
Reserving size (317396) for bucket 7
Calculating Z arrays for bucket 7
Entering block accumulator loop for bucket 7:
Getting block 8 of 59
Reserving size (317396) for bucket 8
Calculating Z arrays for bucket 8
Entering block accumulator loop for bucket 8:
bucket 1: 10%
bucket 4: 10%
bucket 2: 10%
bucket 5: 10%
bucket 6: 10%
bucket 7: 10%
bucket 8: 10%
bucket 3: 10%
bucket 1: 20%
bucket 2: 20%
bucket 4: 20%
bucket 6: 20%
bucket 7: 20%
bucket 8: 20%
bucket 5: 20%
bucket 3: 20%
bucket 1: 30%
bucket 2: 30%
bucket 4: 30%
bucket 6: 30%
bucket 3: 30%
bucket 7: 30%
bucket 8: 30%
bucket 5: 30%
bucket 2: 40%
bucket 1: 40%
bucket 4: 40%
bucket 3: 40%
bucket 6: 40%
bucket 7: 40%
bucket 2: 50%
bucket 8: 40%
bucket 5: 40%
bucket 1: 50%
bucket 4: 50%
bucket 2: 60%
bucket 3: 50%
bucket 6: 50%
bucket 7: 50%
bucket 5: 50%
bucket 8: 50%
bucket 1: 60%
bucket 2: 70%
bucket 4: 60%
bucket 3: 60%
bucket 7: 60%
bucket 6: 60%
bucket 8: 60%
bucket 5: 60%
bucket 1: 70%
bucket 2: 80%
bucket 3: 70%
bucket 4: 70%
bucket 7: 70%
bucket 1: 80%
bucket 6: 70%
bucket 8: 70%
bucket 5: 70%
bucket 2: 90%
bucket 3: 80%
bucket 4: 80%
bucket 1: 90%
bucket 7: 80%
bucket 6: 80%
bucket 5: 80%
bucket 8: 80%
bucket 2: 100%
Sorting block of length 315861 for bucket 2
(Using difference cover)
bucket 3: 90%
bucket 4: 90%
bucket 1: 100%
Sorting block of length 25236 for bucket 1
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 25237 for bucket 1
bucket 6: 90%
bucket 7: 90%
Getting block 9 of 59
Reserving size (317396) for bucket 9
Calculating Z arrays for bucket 9
Entering block accumulator loop for bucket 9:
bucket 8: 90%
bucket 5: 90%
bucket 3: 100%
Sorting block of length 179737 for bucket 3
(Using difference cover)
bucket 4: 100%
Sorting block of length 231987 for bucket 4
(Using difference cover)
bucket 6: 100%
Sorting block of length 192174 for bucket 6
(Using difference cover)
bucket 7: 100%
Sorting block of length 212349 for bucket 7
(Using difference cover)
bucket 9: 10%
bucket 8: 100%
Sorting block of length 240099 for bucket 8
(Using difference cover)
bucket 5: 100%
Sorting block of length 261431 for bucket 5
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 315862 for bucket 2
Sorting block time: 00:00:00
Returning block of 179738 for bucket 3
bucket 9: 20%
Getting block 10 of 59
Reserving size (317396) for bucket 10
Calculating Z arrays for bucket 10
Entering block accumulator loop for bucket 10:
Getting block 11 of 59
Reserving size (317396) for bucket 11
Calculating Z arrays for bucket 11
Entering block accumulator loop for bucket 11:
Sorting block time: 00:00:00
Returning block of 231988 for bucket 4
Sorting block time: 00:00:00
Returning block of 192175 for bucket 6
Sorting block time: 00:00:00
Returning block of 212350 for bucket 7
Getting block 12 of 59
Reserving size (317396) for bucket 12
Calculating Z arrays for bucket 12
Entering block accumulator loop for bucket 12:
Getting block 13 of 59
Reserving size (317396) for bucket 13
Calculating Z arrays for bucket 13
Entering block accumulator loop for bucket 13:
Getting block 14 of 59
Reserving size (317396) for bucket 14
Calculating Z arrays for bucket 14
Entering block accumulator loop for bucket 14:
Sorting block time: 00:00:00
Returning block of 240100 for bucket 8
bucket 9: 30%
bucket 10: 10%
Sorting block time: 00:00:00
Returning block of 261432 for bucket 5
Getting block 15 of 59
Reserving size (317396) for bucket 15
Calculating Z arrays for bucket 15
Entering block accumulator loop for bucket 15:
bucket 11: 10%
Getting block 16 of 59
Reserving size (317396) for bucket 16
Calculating Z arrays for bucket 16
Entering block accumulator loop for bucket 16:
bucket 12: 10%
bucket 13: 10%
bucket 14: 10%
bucket 9: 40%
bucket 10: 20%
bucket 11: 20%
bucket 15: 10%
bucket 16: 10%
bucket 12: 20%
bucket 14: 20%
bucket 13: 20%
bucket 9: 50%
bucket 10: 30%
bucket 11: 30%
bucket 15: 20%
bucket 14: 30%
bucket 12: 30%
bucket 16: 20%
bucket 13: 30%
bucket 9: 60%
bucket 10: 40%
bucket 11: 40%
bucket 15: 30%
bucket 14: 40%
bucket 12: 40%
bucket 9: 70%
bucket 10: 50%
bucket 13: 40%
bucket 16: 30%
bucket 11: 50%
bucket 14: 50%
bucket 15: 40%
bucket 12: 50%
bucket 10: 60%
bucket 9: 80%
bucket 13: 50%
bucket 16: 40%
bucket 14: 60%
bucket 11: 60%
bucket 15: 50%
bucket 10: 70%
bucket 12: 60%
bucket 9: 90%
bucket 13: 60%
bucket 16: 50%
bucket 14: 70%
bucket 11: 70%
bucket 10: 80%
bucket 9: 100%
Sorting block of length 236608 for bucket 9
(Using difference cover)
bucket 12: 70%
bucket 15: 60%
bucket 13: 70%
bucket 16: 60%
bucket 14: 80%
bucket 10: 90%
bucket 11: 80%
bucket 12: 80%
bucket 15: 70%
bucket 13: 80%
bucket 16: 70%
bucket 14: 90%
Sorting block time: 00:00:00
Returning block of 236609 for bucket 9
bucket 10: 100%
Sorting block of length 157060 for bucket 10
(Using difference cover)
bucket 11: 90%
Getting block 17 of 59
Reserving size (317396) for bucket 17
Calculating Z arrays for bucket 17
Entering block accumulator loop for bucket 17:
bucket 12: 90%
bucket 15: 80%
bucket 13: 90%
bucket 16: 80%
bucket 14: 100%
Sorting block of length 153879 for bucket 14
(Using difference cover)
bucket 11: 100%
Sorting block of length 209880 for bucket 11
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 157061 for bucket 10
bucket 12: 100%
Sorting block of length 194732 for bucket 12
(Using difference cover)
bucket 17: 10%
Getting block 18 of 59
Reserving size (317396) for bucket 18
Calculating Z arrays for bucket 18
Entering block accumulator loop for bucket 18:
bucket 15: 90%
bucket 13: 100%
Sorting block of length 287453 for bucket 13
(Using difference cover)
bucket 16: 90%
Sorting block time: 00:00:00
Returning block of 153880 for bucket 14
Getting block 19 of 59
Reserving size (317396) for bucket 19
Calculating Z arrays for bucket 19
Entering block accumulator loop for bucket 19:
bucket 17: 20%
bucket 18: 10%
bucket 15: 100%
Sorting block of length 236203 for bucket 15
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 194733 for bucket 12
bucket 16: 100%
Sorting block of length 250076 for bucket 16
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 209881 for bucket 11
Getting block 20 of 59
Reserving size (317396) for bucket 20
Calculating Z arrays for bucket 20
Entering block accumulator loop for bucket 20:
bucket 19: 10%
Getting block 21 of 59
Reserving size (317396) for bucket 21
Calculating Z arrays for bucket 21
Entering block accumulator loop for bucket 21:
bucket 17: 30%
bucket 18: 20%
Sorting block time: 00:00:00
Returning block of 287454 for bucket 13
Getting block 22 of 59
Reserving size (317396) for bucket 22
Calculating Z arrays for bucket 22
Entering block accumulator loop for bucket 22:
bucket 20: 10%
bucket 19: 20%
Sorting block time: 00:00:00
Returning block of 236204 for bucket 15
bucket 17: 40%
bucket 18: 30%
bucket 21: 10%
Sorting block time: 00:00:00
Returning block of 250077 for bucket 16
Getting block 23 of 59
Reserving size (317396) for bucket 23
Calculating Z arrays for bucket 23
Entering block accumulator loop for bucket 23:
Getting block 24 of 59
Reserving size (317396) for bucket 24
Calculating Z arrays for bucket 24
Entering block accumulator loop for bucket 24:
bucket 22: 10%
bucket 20: 20%
bucket 19: 30%
bucket 17: 50%
bucket 18: 40%
bucket 21: 20%
bucket 23: 10%
bucket 24: 10%
bucket 22: 20%
bucket 20: 30%
bucket 17: 60%
bucket 19: 40%
bucket 18: 50%
bucket 21: 30%
bucket 17: 70%
bucket 22: 30%
bucket 23: 20%
bucket 24: 20%
bucket 20: 40%
bucket 18: 60%
bucket 19: 50%
bucket 21: 40%
bucket 17: 80%
bucket 18: 70%
bucket 23: 30%
bucket 22: 40%
bucket 20: 50%
bucket 24: 30%
bucket 19: 60%
bucket 21: 50%
bucket 17: 90%
bucket 18: 80%
bucket 23: 40%
bucket 22: 50%
bucket 20: 60%
bucket 24: 40%
bucket 19: 70%
bucket 21: 60%
bucket 17: 100%
Sorting block of length 255385 for bucket 17
(Using difference cover)
bucket 18: 90%
bucket 23: 50%
bucket 20: 70%
bucket 22: 60%
bucket 24: 50%
bucket 19: 80%
bucket 21: 70%
bucket 18: 100%
Sorting block of length 193039 for bucket 18
(Using difference cover)
bucket 23: 60%
bucket 24: 60%
bucket 22: 70%
bucket 19: 90%
Sorting block time: 00:00:00
Returning block of 255386 for bucket 17
bucket 20: 80%
bucket 21: 80%
Getting block 25 of 59
Reserving size (317396) for bucket 25
Calculating Z arrays for bucket 25
Entering block accumulator loop for bucket 25:
Sorting block time: 00:00:00
Returning block of 193040 for bucket 18
bucket 23: 70%
Getting block 26 of 59
Reserving size (317396) for bucket 26
Calculating Z arrays for bucket 26
Entering block accumulator loop for bucket 26:
bucket 19: 100%
Sorting block of length 223267 for bucket 19
(Using difference cover)
bucket 22: 80%
bucket 24: 70%
bucket 20: 90%
bucket 21: 90%
bucket 25: 10%
bucket 26: 10%
bucket 23: 80%
bucket 22: 90%
bucket 24: 80%
bucket 25: 20%
bucket 20: 100%
Sorting block of length 317369 for bucket 20
(Using difference cover)
bucket 21: 100%
Sorting block of length 193747 for bucket 21
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 223268 for bucket 19
bucket 26: 20%
bucket 23: 90%
bucket 22: 100%
Sorting block of length 271332 for bucket 22
(Using difference cover)
bucket 24: 90%
bucket 25: 30%
Sorting block time: 00:00:00
Returning block of 193748 for bucket 21
bucket 26: 30%
bucket 23: 100%
Sorting block of length 167037 for bucket 23
(Using difference cover)
bucket 25: 40%
bucket 24: 100%
Sorting block of length 171287 for bucket 24
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 317370 for bucket 20
bucket 26: 40%
Sorting block time: 00:00:00
Returning block of 271333 for bucket 22
bucket 25: 50%
Sorting block time: 00:00:00
Returning block of 167038 for bucket 23
bucket 26: 50%
Sorting block time: 00:00:00
Returning block of 171288 for bucket 24
bucket 25: 60%
bucket 26: 60%
bucket 25: 70%
bucket 25: 80%
bucket 26: 70%
bucket 25: 90%
bucket 26: 80%
bucket 25: 100%
Sorting block of length 296970 for bucket 25
(Using difference cover)
bucket 26: 90%
Sorting block time: 00:00:00
Returning block of 296971 for bucket 25
bucket 26: 100%
Sorting block of length 261601 for bucket 26
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 261602 for bucket 26
Getting block 27 of 59
Reserving size (317396) for bucket 27
Calculating Z arrays for bucket 27
Entering block accumulator loop for bucket 27:
Getting block 28 of 59
Reserving size (317396) for bucket 28
Calculating Z arrays for bucket 28
Entering block accumulator loop for bucket 28:
Getting block 29 of 59
Reserving size (317396) for bucket 29
Calculating Z arrays for bucket 29
Entering block accumulator loop for bucket 29:
Getting block 30 of 59
Reserving size (317396) for bucket 30
Calculating Z arrays for bucket 30
Entering block accumulator loop for bucket 30:
Getting block 31 of 59
Reserving size (317396) for bucket 31
Calculating Z arrays for bucket 31
Entering block accumulator loop for bucket 31:
Getting block 32 of 59
Reserving size (317396) for bucket 32
Calculating Z arrays for bucket 32
Entering block accumulator loop for bucket 32:
Getting block 33 of 59
Reserving size (317396) for bucket 33
Calculating Z arrays for bucket 33
Entering block accumulator loop for bucket 33:
Getting block 34 of 59
Reserving size (317396) for bucket 34
Calculating Z arrays for bucket 34
Entering block accumulator loop for bucket 34:
bucket 27: 10%
bucket 28: 10%
bucket 29: 10%
bucket 32: 10%
bucket 33: 10%
bucket 31: 10%
bucket 30: 10%
bucket 34: 10%
bucket 27: 20%
bucket 28: 20%
bucket 32: 20%
bucket 33: 20%
bucket 29: 20%
bucket 31: 20%
bucket 30: 20%
bucket 34: 20%
bucket 27: 30%
bucket 28: 30%
bucket 33: 30%
bucket 32: 30%
bucket 29: 30%
bucket 31: 30%
bucket 34: 30%
bucket 30: 30%
bucket 28: 40%
bucket 27: 40%
bucket 33: 40%
bucket 32: 40%
bucket 29: 40%
bucket 30: 40%
bucket 31: 40%
bucket 28: 50%
bucket 27: 50%
bucket 34: 40%
bucket 33: 50%
bucket 29: 50%
bucket 32: 50%
bucket 31: 50%
bucket 27: 60%
bucket 30: 50%
bucket 34: 50%
bucket 28: 60%
bucket 33: 60%
bucket 29: 60%
bucket 32: 60%
bucket 27: 70%
bucket 34: 60%
bucket 28: 70%
bucket 33: 70%
bucket 30: 60%
bucket 31: 60%
bucket 32: 70%
bucket 29: 70%
bucket 27: 80%
bucket 34: 70%
bucket 28: 80%
bucket 33: 80%
bucket 31: 70%
bucket 32: 80%
bucket 30: 70%
bucket 29: 80%
bucket 27: 90%
bucket 28: 90%
bucket 34: 80%
bucket 33: 90%
bucket 32: 90%
bucket 31: 80%
bucket 30: 80%
bucket 29: 90%
bucket 28: 100%
Sorting block of length 258899 for bucket 28
(Using difference cover)
bucket 27: 100%
Sorting block of length 103285 for bucket 27
(Using difference cover)
bucket 34: 90%
bucket 32: 100%
Sorting block of length 304022 for bucket 32
(Using difference cover)
bucket 33: 100%
Sorting block of length 220734 for bucket 33
(Using difference cover)
bucket 31: 90%
bucket 30: 90%
bucket 29: 100%
Sorting block of length 298284 for bucket 29
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 103286 for bucket 27
Getting block 35 of 59
Reserving size (317396) for bucket 35
Calculating Z arrays for bucket 35
Entering block accumulator loop for bucket 35:
bucket 34: 100%
Sorting block of length 157583 for bucket 34
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 258900 for bucket 28
bucket 31: 100%
Sorting block of length 291711 for bucket 31
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 220735 for bucket 33
Getting block 36 of 59
Reserving size (317396) for bucket 36
Calculating Z arrays for bucket 36
Entering block accumulator loop for bucket 36:
Getting block 37 of 59
Reserving size (317396) for bucket 37
Calculating Z arrays for bucket 37
Entering block accumulator loop for bucket 37:
bucket 30: 100%
Sorting block of length 243228 for bucket 30
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 304023 for bucket 32
bucket 35: 10%
Sorting block time: 00:00:00
Returning block of 157584 for bucket 34
Getting block 38 of 59
Reserving size (317396) for bucket 38
Calculating Z arrays for bucket 38
Entering block accumulator loop for bucket 38:
Getting block 39 of 59
Reserving size (317396) for bucket 39
Calculating Z arrays for bucket 39
Entering block accumulator loop for bucket 39:
Sorting block time: 00:00:00
Returning block of 298285 for bucket 29
bucket 36: 10%
bucket 37: 10%
Getting block 40 of 59
Reserving size (317396) for bucket 40
Calculating Z arrays for bucket 40
Entering block accumulator loop for bucket 40:
bucket 35: 20%
Sorting block time: 00:00:00
Returning block of 291712 for bucket 31
Sorting block time: 00:00:00
Returning block of 243229 for bucket 30
bucket 38: 10%
bucket 39: 10%
Getting block 41 of 59
Reserving size (317396) for bucket 41
Calculating Z arrays for bucket 41
Entering block accumulator loop for bucket 41:
Getting block 42 of 59
Reserving size (317396) for bucket 42
Calculating Z arrays for bucket 42
Entering block accumulator loop for bucket 42:
bucket 40: 10%
bucket 37: 20%
bucket 36: 20%
bucket 35: 30%
bucket 38: 20%
bucket 39: 20%
bucket 40: 20%
bucket 41: 10%
bucket 42: 10%
bucket 37: 30%
bucket 35: 40%
bucket 36: 30%
bucket 38: 30%
bucket 40: 30%
bucket 41: 20%
bucket 42: 20%
bucket 37: 40%
bucket 39: 30%
bucket 35: 50%
bucket 38: 40%
bucket 40: 40%
bucket 36: 40%
bucket 37: 50%
bucket 41: 30%
bucket 42: 30%
bucket 35: 60%
bucket 39: 40%
bucket 38: 50%
bucket 40: 50%
bucket 37: 60%
bucket 41: 40%
bucket 42: 40%
bucket 36: 50%
bucket 35: 70%
bucket 39: 50%
bucket 40: 60%
bucket 38: 60%
bucket 37: 70%
bucket 41: 50%
bucket 42: 50%
bucket 35: 80%
bucket 40: 70%
bucket 39: 60%
bucket 38: 70%
bucket 36: 60%
bucket 37: 80%
bucket 41: 60%
bucket 42: 60%
bucket 40: 80%
bucket 38: 80%
bucket 35: 90%
bucket 39: 70%
bucket 37: 90%
bucket 36: 70%
bucket 41: 70%
bucket 42: 70%
bucket 38: 90%
bucket 40: 90%
bucket 35: 100%
Sorting block of length 237486 for bucket 35
(Using difference cover)
bucket 37: 100%
Sorting block of length 291568 for bucket 37
(Using difference cover)
bucket 39: 80%
bucket 41: 80%
bucket 42: 80%
bucket 36: 80%
bucket 38: 100%
Sorting block of length 244260 for bucket 38
(Using difference cover)
bucket 40: 100%
Sorting block of length 233272 for bucket 40
(Using difference cover)
bucket 39: 90%
bucket 42: 90%
bucket 41: 90%
Sorting block time: 00:00:00
Returning block of 237487 for bucket 35
Sorting block time: 00:00:00
Returning block of 291569 for bucket 37
bucket 36: 90%
Getting block 43 of 59
Reserving size (317396) for bucket 43
Calculating Z arrays for bucket 43
Entering block accumulator loop for bucket 43:
Getting block 44 of 59
Reserving size (317396) for bucket 44
Calculating Z arrays for bucket 44
Entering block accumulator loop for bucket 44:
Sorting block time: 00:00:00
Returning block of 244261 for bucket 38
Sorting block time: 00:00:00
Returning block of 233273 for bucket 40
Getting block 45 of 59
Reserving size (317396) for bucket 45
Calculating Z arrays for bucket 45
Entering block accumulator loop for bucket 45:
bucket 42: 100%
Sorting block of length 297133 for bucket 42
(Using difference cover)
bucket 41: 100%
Sorting block of length 250351 for bucket 41
(Using difference cover)
Getting block 46 of 59
Reserving size (317396) for bucket 46
Calculating Z arrays for bucket 46
Entering block accumulator loop for bucket 46:
bucket 39: 100%
Sorting block of length 214666 for bucket 39
(Using difference cover)
bucket 36: 100%
Sorting block of length 101213 for bucket 36
(Using difference cover)
bucket 44: 10%
bucket 45: 10%
bucket 46: 10%
bucket 43: 10%
Sorting block time: 00:00:01
Returning block of 101214 for bucket 36
Sorting block time: 00:00:01
Returning block of 250352 for bucket 41
Getting block 47 of 59
Reserving size (317396) for bucket 47
Calculating Z arrays for bucket 47
Entering block accumulator loop for bucket 47:
Sorting block time: 00:00:01
Returning block of 214667 for bucket 39
Sorting block time: 00:00:01
Returning block of 297134 for bucket 42
Getting block 48 of 59
Reserving size (317396) for bucket 48
Calculating Z arrays for bucket 48
Entering block accumulator loop for bucket 48:
Getting block 49 of 59
Reserving size (317396) for bucket 49
Calculating Z arrays for bucket 49
Entering block accumulator loop for bucket 49:
bucket 44: 20%
Getting block 50 of 59
Reserving size (317396) for bucket 50
Calculating Z arrays for bucket 50
Entering block accumulator loop for bucket 50:
bucket 45: 20%
bucket 43: 20%
bucket 46: 20%
bucket 48: 10%
bucket 49: 10%
bucket 47: 10%
bucket 43: 30%
bucket 44: 30%
bucket 45: 30%
bucket 50: 10%
bucket 46: 30%
bucket 43: 40%
bucket 48: 20%
bucket 49: 20%
bucket 44: 40%
bucket 45: 40%
bucket 50: 20%
bucket 47: 20%
bucket 43: 50%
bucket 46: 40%
bucket 48: 30%
bucket 49: 30%
bucket 44: 50%
bucket 45: 50%
bucket 50: 30%
bucket 43: 60%
bucket 47: 30%
bucket 48: 40%
bucket 46: 50%
bucket 49: 40%
bucket 44: 60%
bucket 45: 60%
bucket 43: 70%
bucket 50: 40%
bucket 48: 50%
bucket 47: 40%
bucket 46: 60%
bucket 49: 50%
bucket 44: 70%
bucket 43: 80%
bucket 45: 70%
bucket 50: 50%
bucket 48: 60%
bucket 49: 60%
bucket 46: 70%
bucket 43: 90%
bucket 44: 80%
bucket 45: 80%
bucket 47: 50%
bucket 50: 60%
bucket 48: 70%
bucket 43: 100%
Sorting block of length 300961 for bucket 43
(Using difference cover)
bucket 49: 70%
bucket 44: 90%
bucket 46: 80%
bucket 45: 90%
bucket 47: 60%
bucket 50: 70%
bucket 48: 80%
bucket 44: 100%
Sorting block of length 286470 for bucket 44
(Using difference cover)
bucket 49: 80%
bucket 45: 100%
Sorting block of length 309474 for bucket 45
(Using difference cover)
bucket 46: 90%
bucket 50: 80%
Sorting block time: 00:00:00
Returning block of 300962 for bucket 43
bucket 47: 70%
bucket 48: 90%
bucket 49: 90%
Getting block 51 of 59
Reserving size (317396) for bucket 51
Calculating Z arrays for bucket 51
Entering block accumulator loop for bucket 51:
bucket 46: 100%
Sorting block of length 209376 for bucket 46
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 286471 for bucket 44
Sorting block time: 00:00:00
Returning block of 309475 for bucket 45
bucket 50: 90%
bucket 48: 100%
Sorting block of length 188712 for bucket 48
(Using difference cover)
Getting block 52 of 59
Reserving size (317396) for bucket 52
Calculating Z arrays for bucket 52
Entering block accumulator loop for bucket 52:
bucket 47: 80%
Getting block 53 of 59
Reserving size (317396) for bucket 53
Calculating Z arrays for bucket 53
Entering block accumulator loop for bucket 53:
bucket 49: 100%
Sorting block of length 317074 for bucket 49
(Using difference cover)
bucket 51: 10%
Sorting block time: 00:00:00
Returning block of 209377 for bucket 46
bucket 50: 100%
Sorting block of length 272545 for bucket 50
(Using difference cover)
Getting block 54 of 59
Reserving size (317396) for bucket 54
Calculating Z arrays for bucket 54
Entering block accumulator loop for bucket 54:
Sorting block time: 00:00:00
Returning block of 188713 for bucket 48
bucket 53: 10%
Getting block 55 of 59
Reserving size (317396) for bucket 55
Calculating Z arrays for bucket 55
bucket 51: 20%
bucket 52: 10%
Entering block accumulator loop for bucket 55:
bucket 47: 90%
Sorting block time: 00:00:00
Returning block of 317075 for bucket 49
bucket 54: 10%
bucket 52: 20%
bucket 53: 20%
Getting block 56 of 59
Reserving size (317396) for bucket 56
Calculating Z arrays for bucket 56
Entering block accumulator loop for bucket 56:
bucket 51: 30%
bucket 55: 10%
Sorting block time: 00:00:00
Returning block of 272546 for bucket 50
Getting block 57 of 59
Reserving size (317396) for bucket 57
Calculating Z arrays for bucket 57
Entering block accumulator loop for bucket 57:
bucket 47: 100%
Sorting block of length 266355 for bucket 47
(Using difference cover)
bucket 52: 30%
bucket 54: 20%
bucket 56: 10%
bucket 51: 40%
bucket 53: 30%
bucket 55: 20%
bucket 57: 10%
bucket 52: 40%
bucket 56: 20%
bucket 54: 30%
bucket 51: 50%
bucket 53: 40%
bucket 55: 30%
bucket 57: 20%
Sorting block time: 00:00:00
Returning block of 266356 for bucket 47
bucket 52: 50%
bucket 56: 30%
bucket 54: 40%
bucket 53: 50%
bucket 51: 60%
Getting block 58 of 59
Reserving size (317396) for bucket 58
Calculating Z arrays for bucket 58
Entering block accumulator loop for bucket 58:
bucket 55: 40%
bucket 57: 30%
bucket 56: 40%
bucket 52: 60%
bucket 54: 50%
bucket 51: 70%
bucket 53: 60%
bucket 55: 50%
bucket 57: 40%
bucket 58: 10%
bucket 56: 50%
bucket 52: 70%
bucket 54: 60%
bucket 51: 80%
bucket 53: 70%
bucket 55: 60%
bucket 57: 50%
bucket 56: 60%
bucket 52: 80%
bucket 51: 90%
bucket 54: 70%
bucket 58: 20%
bucket 55: 70%
bucket 53: 80%
bucket 57: 60%
bucket 56: 70%
bucket 52: 90%
bucket 54: 80%
bucket 51: 100%
Sorting block of length 111013 for bucket 51
(Using difference cover)
bucket 55: 80%
bucket 58: 30%
bucket 53: 90%
bucket 57: 70%
bucket 56: 80%
bucket 52: 100%
Sorting block of length 297672 for bucket 52
(Using difference cover)
bucket 54: 90%
bucket 55: 90%
Sorting block time: 00:00:00
Returning block of 111014 for bucket 51
Getting block 59 of 59
Reserving size (317396) for bucket 59
Calculating Z arrays for bucket 59
Entering block accumulator loop for bucket 59:
bucket 53: 100%
Sorting block of length 205886 for bucket 53
(Using difference cover)
bucket 57: 80%
bucket 56: 90%
bucket 58: 40%
bucket 59: 10%
Sorting block time: 00:00:00
Returning block of 297673 for bucket 52
bucket 55: 100%
Sorting block of length 242121 for bucket 55
(Using difference cover)
bucket 57: 90%
bucket 56: 100%
Sorting block of length 187618 for bucket 56
(Using difference cover)
bucket 59: 20%
bucket 54: 100%
Sorting block of length 150210 for bucket 54
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 205887 for bucket 53
bucket 58: 50%
bucket 59: 30%
bucket 57: 100%
Sorting block of length 281318 for bucket 57
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 150211 for bucket 54
Sorting block time: 00:00:00
Returning block of 187619 for bucket 56
bucket 59: 40%
bucket 58: 60%
Sorting block time: 00:00:00
Returning block of 242122 for bucket 55
bucket 59: 50%
bucket 58: 70%
Sorting block time: 00:00:00
Returning block of 281319 for bucket 57
bucket 59: 60%
bucket 58: 80%
bucket 59: 70%
bucket 58: 90%
bucket 59: 80%
bucket 58: 100%
Sorting block of length 125664 for bucket 58
(Using difference cover)
bucket 59: 90%
Sorting block time: 00:00:00
Returning block of 125665 for bucket 58
bucket 59: 100%
Sorting block of length 306213 for bucket 59
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 306214 for bucket 59
Exited GFM loop
fchr[A]: 0
fchr[C]: 5036868
fchr[G]: 6776772
fchr[T]: 8516403
fchr[$]: 13542234
Exiting GFM::buildToDisk()
Returning from initFromVector
Wrote 8743985 bytes to primary GFM file: hisat2_index.1.ht2
Wrote 3385564 bytes to secondary GFM file: hisat2_index.2.ht2
Re-opening _in1 and _in2 as input streams
Returning from GFM constructor
Returning from initFromVector
Wrote 11673573 bytes to primary GFM file: hisat2_index.5.ht2
Wrote 3394706 bytes to secondary GFM file: hisat2_index.6.ht2
Re-opening _in5 and _in5 as input streams
Returning from HGFM constructor
Headers:
len: 13542234
gbwtLen: 13542235
nodes: 13542235
sz: 3385559
gbwtSz: 3385559
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 0
eftabSz: 0
ftabLen: 1048577
ftabSz: 4194308
offsLen: 846390
offsSz: 3385560
lineSz: 64
sideSz: 64
sideGbwtSz: 48
sideGbwtLen: 192
numSides: 70533
numLines: 70533
gbwtTotLen: 4514112
gbwtTotSz: 4514112
reverse: 0
linearFM: Yes
Total time for call to driver() for forward index: 00:00:12
+ mkdir -p output.prinseq
+ for i in $r1gz
+ xargs '-d\n' -I '{}' -P 8 bash -c '{}'
++ echo input_1//S_l1_1.fq.gz
++ egrep '_1[.]f(ast|)q[.]gz$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo input_1//S_l1_1.fq.gz
++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/'
+ j=input_1//S_l1_2.fq.gz
++ basename input_1//S_l1_1.fq.gz .gz
+ i2=S_l1_1.fq
++ basename input_1//S_l1_2.fq.gz .gz
+ j2=S_l1_2.fq
++ basename input_1//S_l1_1.fq.gz
+ echo zcat input_1//S_l1_1.fq.gz '>' 'S_l1_1.fq;' zcat input_1//S_l1_2.fq.gz '>' 'S_l1_2.fq;' 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list;' podman run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/prinseq:0.20.4 prinseq-lite.pl -fastq S_l1_1.fq -fastq2 S_l1_2.fq -out_good output.prinseq/S_l1_1.fq -out_bad null -out_format 3 -trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window 5 '>' log.prinseq.S_l1_1.fq.gz '2>&1' ';' mv output.prinseq/S_l1_1.fq_1.fastq 'output.prinseq/S_l1_1.fq;' mv output.prinseq/S_l1_1.fq_2.fastq 'output.prinseq/S_l1_2.fq;rm' -f S_l1_1.fq S_l1_2.fq
+ rm -f output.prinseq/S_l1_1.fq_1_singletons.fastq output.prinseq/S_l1_1.fq_2_singletons.fastq
++ find output.prinseq/
++ egrep '(_R1.*|_1)[.]f(ast|)q$'
+ r1=output.prinseq/S_l1_1.fq
+ echo ''
+ for i in $r1
+ xargs '-d\n' -I '{}' -P 1 bash -c '{}'
++ echo output.prinseq/S_l1_1.fq
++ egrep '_1[.]f(ast|)q$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo output.prinseq/S_l1_1.fq
++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/'
+ j=output.prinseq/S_l1_2.fq
++ basename output.prinseq/S_l1_1.fq
++ basename output.prinseq/S_l1_1.fq
++ basename output.prinseq/S_l1_1.fq
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list;' podman run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 hisat2 --rna-strandness RF -p 8 --dta --dta-cufflinks -x hisat2_index -1 output.prinseq/S_l1_1.fq -2 output.prinseq/S_l1_2.fq --rg-id output.prinseq/S_l1_1.fq --rg SM:output.prinseq/S_l1_1.fq '2>' log.hisat2.S_l1_1.fq '|(PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list;' podman run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools sort -@ 8 -o S_l1_1.fq.bam ');' 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list;' podman run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools index S_l1_1.fq.bam
++ basename output.prinseq/S_l1_1.fq
+ echo S_l1_1.fq.bam
[bam_sort_core] merging from 24 files and 8 in-memory blocks...
++ awk '{ORS=","; print $0}' bamlist
++ sed 's/^,//; s/,$//'
+ bamlist=S_l1_1.fq.bam
+ FUNC_RUN_PODMAN c2997108/ubuntu-18:braker2_hisat2_5 braker.pl '--genome='\''input_2/parasite.fa.ref.fa'\''' --species=run1 '--bam='\''S_l1_1.fq.bam'\''' ''
+ PP_RUN_IMAGE=c2997108/ubuntu-18:braker2_hisat2_5
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20231113_212634_649_18183
+ echo pp20231113_212634_649_18183
++ echo c2997108/ubuntu-18:braker2_hisat2_5
++ awk -F/ '{if(NF==2){$0="docker.io/"$0}; print $0}'
+ PP_RUN_IMAGE=docker.io/c2997108/ubuntu-18:braker2_hisat2_5
+ podman run --name pp20231113_212634_649_18183 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -i --rm docker.io/c2997108/ubuntu-18:braker2_hisat2_5 braker.pl '--genome='\''input_2/parasite.fa.ref.fa'\''' --species=run1 '--bam='\''S_l1_1.fq.bam'\''' ''
Error: crun: executable file `braker.pl` not found in $PATH: No such file or directory: OCI runtime attempted to invoke a command that was not found
PID: 2523905
pp runtime error.
Checking the realpath of input files.
0 input_1/
1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/input_1/S_l1_1.fq.gz
1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/input_1/S_l1_2.fq.gz
0 input_2/parasite.fa
0
0
/home/yoshitake.kazutoshi/work -> /data/yoshitake.kazutoshi/work
/home/yoshitake.kazutoshi/work/pp-dev -> /data/yoshitake.kazutoshi/work/pp-dev
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3
/data/yoshitake.kazutoshi/work
/data/yoshitake.kazutoshi/work/pp-dev
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3
biocontainers/emboss:v6.6.0dfsg-7b1-deb_cv1 c2997108/braker:3 c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 c2997108/ubuntu-18:braker2_hisat2_5 centos:centos6 quay.io/biocontainers/gffread:0.12.7--h9a82719_0 quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 quay.io/biocontainers/prinseq:0.20.4 quay.io/biocontainers/samtools:1.9--h10a08f8_12 quay.io/biocontainers/seqkit:0.12.1--0
using podman
++ podman pull centos:centos6
Trying to pull quay.io/centos/centos:centos6...
Getting image source signatures
Copying blob sha256:ff50d722b38227ec8f2bbf0cdbce428b66745077c173d8117d91376128fa532e
Copying config sha256:d0957ffdf8a2ea8c8925903862b65a1b6850dbb019f88d45e927d3d5a3fa0c31
Writing manifest to image destination
Storing signatures
d0957ffdf8a2ea8c8925903862b65a1b6850dbb019f88d45e927d3d5a3fa0c31
++ set +ex
+ set -o pipefail
++ find input_1//
++ egrep '(_R1.*|_1)[.]f(ast|)q$'
++ echo ''
+ r1=
++ find input_1//
++ egrep '(_R1.*|_1)[.]f(ast|)q[.]gz$'
+ r1gz=input_1//S_l1_1.fq.gz
+ '[' input_1//S_l1_1.fq.gz = '' ']'
+ r2=
++ for i in $r1gz
+++ echo input_1//S_l1_1.fq.gz
+++ egrep '_1[.]f(ast|)q[.]gz$'
+++ wc -l
++ '[' 1 = 1 ']'
++ echo input_1//S_l1_1.fq.gz
++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/'
+ r2gz=input_1//S_l1_2.fq.gz
+ echo '#Check paired-end'
#Check paired-end
+ ls input_1//S_l1_2.fq.gz
++ echo input_2/parasite.fa
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
+ awk '{if($0~"^>"){sub(/ .*/,"",$0)}; print $0}' input_2/parasite.fa
+ sed 's/\r//'
+ input_2=input_2/parasite.fa.ref.fa
+ mkdir -p output.prinseq
+ for i in $r1gz
++ echo input_1//S_l1_1.fq.gz
++ egrep '_1[.]f(ast|)q[.]gz$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo input_1//S_l1_1.fq.gz
++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/'
+ j=input_1//S_l1_2.fq.gz
++ basename input_1//S_l1_1.fq.gz .gz
+ i2=S_l1_1.fq
++ basename input_1//S_l1_2.fq.gz .gz
+ j2=S_l1_2.fq
++ basename input_1//S_l1_1.fq.gz
+ echo zcat input_1//S_l1_1.fq.gz '>' 'S_l1_1.fq;' zcat input_1//S_l1_2.fq.gz '>' 'S_l1_2.fq;' 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list;' podman run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/prinseq:0.20.4 prinseq-lite.pl -fastq S_l1_1.fq -fastq2 S_l1_2.fq -out_good output.prinseq/S_l1_1.fq -out_bad null -out_format 3 -trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window 5 '>' log.prinseq.S_l1_1.fq.gz '2>&1' ';' mv output.prinseq/S_l1_1.fq_1.fastq 'output.prinseq/S_l1_1.fq;' mv output.prinseq/S_l1_1.fq_2.fastq 'output.prinseq/S_l1_2.fq;rm' -f S_l1_1.fq S_l1_2.fq
zcat input_1//S_l1_1.fq.gz > S_l1_1.fq; zcat input_1//S_l1_2.fq.gz > S_l1_2.fq; PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list; podman run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/prinseq:0.20.4 prinseq-lite.pl -fastq S_l1_1.fq -fastq2 S_l1_2.fq -out_good output.prinseq/S_l1_1.fq -out_bad null -out_format 3 -trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window 5 > log.prinseq.S_l1_1.fq.gz 2>&1 ; mv output.prinseq/S_l1_1.fq_1.fastq output.prinseq/S_l1_1.fq; mv output.prinseq/S_l1_1.fq_2.fastq output.prinseq/S_l1_2.fq;rm -f S_l1_1.fq S_l1_2.fq
++ find output.prinseq/
++ egrep '(_R1.*|_1)[.]f(ast|)q$'
+ r1=output.prinseq/S_l1_1.fq
+ echo ''
+ for i in $r1
++ echo output.prinseq/S_l1_1.fq
++ egrep '_1[.]f(ast|)q$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo output.prinseq/S_l1_1.fq
++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/'
+ j=output.prinseq/S_l1_2.fq
++ basename output.prinseq/S_l1_1.fq
++ basename output.prinseq/S_l1_1.fq
++ basename output.prinseq/S_l1_1.fq
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list;' podman run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 hisat2 --rna-strandness RF -p 8 --dta --dta-cufflinks -x hisat2_index -1 output.prinseq/S_l1_1.fq -2 output.prinseq/S_l1_2.fq --rg-id output.prinseq/S_l1_1.fq --rg SM:output.prinseq/S_l1_1.fq '2>' log.hisat2.S_l1_1.fq '|(PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list;' podman run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools sort -@ 8 -o S_l1_1.fq.bam ');' 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list;' podman run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools index S_l1_1.fq.bam
PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list; podman run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 hisat2 --rna-strandness RF -p 8 --dta --dta-cufflinks -x hisat2_index -1 output.prinseq/S_l1_1.fq -2 output.prinseq/S_l1_2.fq --rg-id output.prinseq/S_l1_1.fq --rg SM:output.prinseq/S_l1_1.fq 2> log.hisat2.S_l1_1.fq |(PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list; podman run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools sort -@ 8 -o S_l1_1.fq.bam ); PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list; podman run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools index S_l1_1.fq.bam
++ basename output.prinseq/S_l1_1.fq
+ echo S_l1_1.fq.bam
++ awk '{ORS=","; print $0}' bamlist
++ sed 's/^,//; s/,$//'
+ bamlist=S_l1_1.fq.bam
+ FUNC_RUN_PODMAN c2997108/braker:3 braker.pl --genome=input_2/parasite.fa.ref.fa --species=run1 --bam=S_l1_1.fq.bam ''
+ PP_RUN_IMAGE=c2997108/braker:3
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20231113_213931_362_22257
+ echo pp20231113_213931_362_22257
++ echo c2997108/braker:3
++ awk -F/ '{if(NF==2){$0="docker.io/"$0}; print $0}'
+ PP_RUN_IMAGE=docker.io/c2997108/braker:3
+ podman run --name pp20231113_213931_362_22257 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -i --rm docker.io/c2997108/braker:3 braker.pl --genome=input_2/parasite.fa.ref.fa --species=run1 --bam=S_l1_1.fq.bam ''
#**********************************************************************************
# BRAKER CONFIGURATION
#**********************************************************************************
# BRAKER CALL: /opt/BRAKER/scripts/braker.pl --genome=input_2/parasite.fa.ref.fa --species=run1 --bam=S_l1_1.fq.bam
# Mon Nov 13 12:39:32 2023: braker.pl version 3.0.5
# Mon Nov 13 12:39:32 2023: ERROR: in file /opt/BRAKER/scripts/braker.pl at line 825
Do not have write permission for /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3.
Please use command 'chmod' to reset permissions, or specify another working directory with option --workingdir=...
PID: 2618332
pp runtime error.
Checking the realpath of input files.
0 input_1/
1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/input_1/S_l1_1.fq.gz
1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/input_1/S_l1_2.fq.gz
0 input_2/parasite.fa
0
0
/home/yoshitake.kazutoshi/work -> /data/yoshitake.kazutoshi/work
/home/yoshitake.kazutoshi/work/pp-dev -> /data/yoshitake.kazutoshi/work/pp-dev
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3
/data/yoshitake.kazutoshi/work
/data/yoshitake.kazutoshi/work/pp-dev
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3
biocontainers/emboss:v6.6.0dfsg-7b1-deb_cv1 c2997108/braker:3 c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 c2997108/ubuntu-18:braker2_hisat2_5 centos:centos6 quay.io/biocontainers/gffread:0.12.7--h9a82719_0 quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 quay.io/biocontainers/prinseq:0.20.4 quay.io/biocontainers/samtools:1.9--h10a08f8_12 quay.io/biocontainers/seqkit:0.12.1--0
using podman
++ podman pull centos:centos6
Trying to pull quay.io/centos/centos:centos6...
Error: parsing image configuration: Get "http://m32s:5001/v2/centos/centos/blobs/sha256:d0957ffdf8a2ea8c8925903862b65a1b6850dbb019f88d45e927d3d5a3fa0c31": dial tcp: lookup m32s on 192.168.200.201:53: no such host
PID: 2622182
pp runtime error.
Checking the realpath of input files.
0 input_1/
1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/input_1/S_l1_1.fq.gz
1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/input_1/S_l1_2.fq.gz
0 input_2/parasite.fa
0
0
/home/yoshitake.kazutoshi/work -> /data/yoshitake.kazutoshi/work
/home/yoshitake.kazutoshi/work/pp-dev -> /data/yoshitake.kazutoshi/work/pp-dev
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3
/data/yoshitake.kazutoshi/work
/data/yoshitake.kazutoshi/work/pp-dev
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3
biocontainers/emboss:v6.6.0dfsg-7b1-deb_cv1 c2997108/braker:3 c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 c2997108/ubuntu-18:braker2_hisat2_5 centos:centos6 quay.io/biocontainers/gffread:0.12.7--h9a82719_0 quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 quay.io/biocontainers/prinseq:0.20.4 quay.io/biocontainers/samtools:1.9--h10a08f8_12 quay.io/biocontainers/seqkit:0.12.1--0
using podman
++ podman pull centos:centos6
Trying to pull quay.io/centos/centos:centos6...
Getting image source signatures
Copying blob sha256:ff50d722b38227ec8f2bbf0cdbce428b66745077c173d8117d91376128fa532e
Copying config sha256:d0957ffdf8a2ea8c8925903862b65a1b6850dbb019f88d45e927d3d5a3fa0c31
Writing manifest to image destination
Storing signatures
d0957ffdf8a2ea8c8925903862b65a1b6850dbb019f88d45e927d3d5a3fa0c31
++ set +ex
+ set -o pipefail
++ find input_1//
++ egrep '(_R1.*|_1)[.]f(ast|)q$'
++ echo ''
+ r1=
++ find input_1//
++ egrep '(_R1.*|_1)[.]f(ast|)q[.]gz$'
+ r1gz=input_1//S_l1_1.fq.gz
+ '[' input_1//S_l1_1.fq.gz = '' ']'
+ r2=
++ for i in $r1gz
+++ echo input_1//S_l1_1.fq.gz
+++ egrep '_1[.]f(ast|)q[.]gz$'
+++ wc -l
++ '[' 1 = 1 ']'
++ echo input_1//S_l1_1.fq.gz
++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/'
+ r2gz=input_1//S_l1_2.fq.gz
+ echo '#Check paired-end'
#Check paired-end
+ ls input_1//S_l1_2.fq.gz
++ echo input_2/parasite.fa
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
+ awk '{if($0~"^>"){sub(/ .*/,"",$0)}; print $0}' input_2/parasite.fa
+ sed 's/\r//'
+ input_2=input_2/parasite.fa.ref.fa
+ mkdir -p output.prinseq
+ for i in $r1gz
++ echo input_1//S_l1_1.fq.gz
++ egrep '_1[.]f(ast|)q[.]gz$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo input_1//S_l1_1.fq.gz
++ sed 's/_1[.]f\(ast\|\)q[.]gz/_2.f\1q.gz/'
+ j=input_1//S_l1_2.fq.gz
++ basename input_1//S_l1_1.fq.gz .gz
+ i2=S_l1_1.fq
++ basename input_1//S_l1_2.fq.gz .gz
+ j2=S_l1_2.fq
++ basename input_1//S_l1_1.fq.gz
+ echo zcat input_1//S_l1_1.fq.gz '>' 'S_l1_1.fq;' zcat input_1//S_l1_2.fq.gz '>' 'S_l1_2.fq;' 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list;' podman run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/prinseq:0.20.4 prinseq-lite.pl -fastq S_l1_1.fq -fastq2 S_l1_2.fq -out_good output.prinseq/S_l1_1.fq -out_bad null -out_format 3 -trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window 5 '>' log.prinseq.S_l1_1.fq.gz '2>&1' ';' mv output.prinseq/S_l1_1.fq_1.fastq 'output.prinseq/S_l1_1.fq;' mv output.prinseq/S_l1_1.fq_2.fastq 'output.prinseq/S_l1_2.fq;rm' -f S_l1_1.fq S_l1_2.fq
zcat input_1//S_l1_1.fq.gz > S_l1_1.fq; zcat input_1//S_l1_2.fq.gz > S_l1_2.fq; PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list; podman run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/prinseq:0.20.4 prinseq-lite.pl -fastq S_l1_1.fq -fastq2 S_l1_2.fq -out_good output.prinseq/S_l1_1.fq -out_bad null -out_format 3 -trim_tail_right 5 -trim_qual_right 20 -ns_max_p 20 -min_len 30 -trim_qual_window 5 > log.prinseq.S_l1_1.fq.gz 2>&1 ; mv output.prinseq/S_l1_1.fq_1.fastq output.prinseq/S_l1_1.fq; mv output.prinseq/S_l1_1.fq_2.fastq output.prinseq/S_l1_2.fq;rm -f S_l1_1.fq S_l1_2.fq
++ find output.prinseq/
++ egrep '(_R1.*|_1)[.]f(ast|)q$'
+ r1=output.prinseq/S_l1_1.fq
+ echo ''
+ for i in $r1
++ echo output.prinseq/S_l1_1.fq
++ egrep '_1[.]f(ast|)q$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo output.prinseq/S_l1_1.fq
++ sed 's/_1[.]f\(ast\|\)q/_2.f\1q/'
+ j=output.prinseq/S_l1_2.fq
++ basename output.prinseq/S_l1_1.fq
++ basename output.prinseq/S_l1_1.fq
++ basename output.prinseq/S_l1_1.fq
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list;' podman run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 hisat2 --rna-strandness RF -p 8 --dta --dta-cufflinks -x hisat2_index -1 output.prinseq/S_l1_1.fq -2 output.prinseq/S_l1_2.fq --rg-id output.prinseq/S_l1_1.fq --rg SM:output.prinseq/S_l1_1.fq '2>' log.hisat2.S_l1_1.fq '|(PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list;' podman run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools sort -@ 8 -o S_l1_1.fq.bam ');' 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list;' podman run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools index S_l1_1.fq.bam
PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list; podman run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/hisat2:2.2.0--py36hf0b53f7_4 hisat2 --rna-strandness RF -p 8 --dta --dta-cufflinks -x hisat2_index -1 output.prinseq/S_l1_1.fq -2 output.prinseq/S_l1_2.fq --rg-id output.prinseq/S_l1_1.fq --rg SM:output.prinseq/S_l1_1.fq 2> log.hisat2.S_l1_1.fq |(PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list; podman run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools sort -@ 8 -o S_l1_1.fq.bam ); PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/pp-podman-list; podman run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm quay.io/biocontainers/samtools:1.9--h10a08f8_12 samtools index S_l1_1.fq.bam
++ basename output.prinseq/S_l1_1.fq
+ echo S_l1_1.fq.bam
++ awk '{ORS=","; print $0}' bamlist
++ sed 's/^,//; s/,$//'
+ bamlist=S_l1_1.fq.bam
+ FUNC_RUN_PODMAN c2997108/braker:3 braker.pl --genome=input_2/parasite.fa.ref.fa --species=run1 --bam=S_l1_1.fq.bam ''
+ PP_RUN_IMAGE=c2997108/braker:3
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20231113_214311_517_11050
+ echo pp20231113_214311_517_11050
++ echo c2997108/braker:3
++ awk -F/ '{if(NF==2){$0="docker.io/"$0}; print $0}'
+ PP_RUN_IMAGE=docker.io/c2997108/braker:3
+ podman run --name pp20231113_214311_517_11050 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3 -u root -i --rm docker.io/c2997108/braker:3 braker.pl --genome=input_2/parasite.fa.ref.fa --species=run1 --bam=S_l1_1.fq.bam ''
# Mon Nov 13 12:43:12 2023: Log information is stored in file /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~BRAKER3/braker/braker.log