/home/yoshitake.kazutoshi/files/m256y/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/pp 'trimming~sickle-pe' -c 8 -m 32 input_1/test_1.fq input_2/test_2.fq
Checking the realpath of input files.
1
script: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/PortablePipeline/PortablePipeline/scripts/trimming~sickle-pe
Containers: centos:centos6 quay.io/biocontainers/sickle-trim:1.33--2
using docker
++ set -o pipefail
+ set -eux
+ set -o pipefail
++ echo input_1/test_1.fq
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
++ echo input_2/test_2.fq
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
+ FUNC_RUN_DOCKER quay.io/biocontainers/sickle-trim:1.33--2 sickle pe -f input_1/test_1.fq -r input_2/test_2.fq -t sanger -o output.sickle_1.fastq -p output.sickle_2.fastq -s output.sickle_single.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_094417_555_31823
+ echo pp20241105_094417_555_31823
++ id -u
++ id -g
+ docker run --name pp20241105_094417_555_31823 -v /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/trimming~sickle-pe:/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/trimming~sickle-pe -w /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/trimming~sickle-pe -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 pe -f input_1/test_1.fq -r input_2/test_2.fq -t sanger -o output.sickle_1.fastq -p output.sickle_2.fastq -s output.sickle_single.fastq

FastQ paired records kept: 19260 (9630 pairs)
FastQ single records kept: 369 (from PE1: 369, from PE2: 0)
FastQ paired records discarded: 2 (1 pairs)
FastQ single records discarded: 369 (from PE1: 0, from PE2: 369)

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