preprocessing~extract-only-specific-entries-in-FASTA

input_1:FASTA file

input_1/test.fa

>ERR8701940.1 1 length=57
GCCGGTAAAACTCGTGCCAGCAAAAACGCTTAAACCGGGATTAGATACCCCGCTATG
>ERR8701940.2 2 length=57
GCCGGTAAAACTCGTGCCAGCAAAAGCGCTTAAACTGGGATTAGATACCCCGCTATG
>ERR8701940.3 3 length=57
GCCGGTAAAACTCGTGCCAGCAAAAACGCTTAAACTGGGATTAGATACCCCACTATG
>ERR8701940.4 4 length=57
GCCGGTAAAACTCGTGCCAGCAAAAACGCTTAAACTGGGATTAGATACCCCACTATG
>ERR8701940.5 5 length=57
GCCGGTATAACTCGTGCCAGCAAAAACGCTTAAACTGGGATTAGATACCCCACTATG

input_2:entry list

input_2/test.txt

ERR8701940.2

Command

Output

test.test.fasta

>ERR8701940.2 2 length=57
GCCGGTAAAACTCGTGCCAGCAAAAGCGCTTAAACTGGGATTAGATACCCCGCTATG

Log

pp preprocessing~extract-only-specific-entries-in-FASTA -c 8 -m 32 input_1/test.fa input_2/test.txt
PID: 124745
/home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/pp 'preprocessing~extract-only-specific-entries-in-FASTA' -c 8 -m 32 input_1/test.fa input_2/test.txt
Checking the realpath of input files.
1
script: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/preprocessing~extract-only-specific-entries-in-FASTA
Containers: c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 centos:centos6
using docker
++ set -o pipefail
+ set -eux
+ set -o pipefail
+ fasta=input_1/test.fa
+ table=input_2/test.txt
++ basename input_1/test
++ basename input_2/test
+ output=test.test.fasta
+ sed 's/\r//' input_2/test.txt
+ FUNC_RUN_DOCKER c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 /usr/local/trinityrnaseq-Trinity-v2.8.5/util/support_scripts/fasta_to_tab.pl input_1/test.fa
+ PP_RUN_IMAGE=c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
+ FUNC_RUN_DOCKER c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 awk '-F\t' '
FILENAME==ARGV[1]{split($1,arr," "); flag[arr[1]]=1}
FILENAME==ARGV[2]{split($1,arr," "); if(flag[arr[1]]==1){print ">"$1; print $2}}
' input_2/test.txt.temp /dev/stdin
+ PP_RUN_IMAGE=c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20250604_232735_506_20045
+ echo pp20250604_232735_506_20045
+ PPDOCNAME=pp20250604_232735_506_3900
+ echo pp20250604_232735_506_3900
++ id -u
++ id -u
++ id -g
++ id -g
+ docker run --name pp20250604_232735_506_20045 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/preprocessing~extract-only-specific-entries-in-FASTA:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/preprocessing~extract-only-specific-entries-in-FASTA -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/preprocessing~extract-only-specific-entries-in-FASTA -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 /usr/local/trinityrnaseq-Trinity-v2.8.5/util/support_scripts/fasta_to_tab.pl input_1/test.fa
+ docker run --name pp20250604_232735_506_3900 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/preprocessing~extract-only-specific-entries-in-FASTA:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/preprocessing~extract-only-specific-entries-in-FASTA -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/preprocessing~extract-only-specific-entries-in-FASTA -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_3-kegg_2 awk '-F\t' '
FILENAME==ARGV[1]{split($1,arr," "); flag[arr[1]]=1}
FILENAME==ARGV[2]{split($1,arr," "); if(flag[arr[1]]==1){print ">"$1; print $2}}
' input_2/test.txt.temp /dev/stdin
+ post_processing
+ '[' 1 = 1 ']'
+ rm -f /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/preprocessing~extract-only-specific-entries-in-FASTA/pp-singularity-flag
+ '[' '' = y ']'
+ echo 0
+ exit