/home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/pp 'trimming~sickle-se' -c 8 -m 32 input_1/SRR27458461.fastq.gz
Checking the realpath of input files.
1
script: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/trimming~sickle-se
Containers: centos:centos6 quay.io/biocontainers/sickle-trim:1.33--2
using docker
++ set -o pipefail
+ set -eux
+ set -o pipefail
++ echo input_1/SRR27458461.fastq.gz
++ grep '[.]gz$'
++ wc -l
+ '[' 1 = 1 ']'
+ FUNC_RUN_DOCKER quay.io/biocontainers/sickle-trim:1.33--2 gzip -dc input_1/SRR27458461.fastq.gz
++ echo input_1/SRR27458461.fastq.gz
++ sed 's/[.]gz$//'
+ PP_RUN_IMAGE=quay.io/biocontainers/sickle-trim:1.33--2
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20241105_093215_861_20207
+ echo pp20241105_093215_861_20207
++ id -u
++ id -g
+ docker run --name pp20241105_093215_861_20207 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/trimming~sickle-se:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/trimming~sickle-se -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/trimming~sickle-se -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/sickle-trim:1.33--2 gzip -dc input_1/SRR27458461.fastq.gz
++ echo input_1/SRR27458461.fastq.gz
++ sed 's/[.]gz$//'
+ input_1=input_1/SRR27458461.fastq
+ FUNC_RUN_DOCKER quay.io/biocontainers/sickle-trim:1.33--2 sickle se -f input_1/SRR27458461.fastq -t sanger -q 15 -l 5000 -o output.sickle.fastq
+ PP_RUN_IMAGE=quay.io/biocontainers/sickle-trim:1.33--2
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20241105_093223_390_14713
+ echo pp20241105_093223_390_14713
++ id -u
++ id -g
+ docker run --name pp20241105_093223_390_14713 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/trimming~sickle-se:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/trimming~sickle-se -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/trimming~sickle-se -v /suikou/files/m256y/yoshitake.kazutoshi:/suikou/files/m256y/yoshitake.kazutoshi -u 2007:600 -i --rm quay.io/biocontainers/sickle-trim:1.33--2 sickle se -f input_1/SRR27458461.fastq -t sanger -q 15 -l 5000 -o output.sickle.fastq

FastQ records kept: 25430
FastQ records discarded: 8842

+ post_processing
+ '[' 1 = 1 ']'
+ rm -f /home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/test/trimming~sickle-se/pp-singularity-flag
+ '[' '' = y ']'
+ echo 0
+ exit