preprocessing~download-SRA-FASTQ

input_1:SRR list

input_1/list.txt

ERR8701941
ERR8701940

Command

Output

fastq/ERR8701940_1.fastq.gz

fastq/ERR8701940_2.fastq.gz

Log

pp preprocessing~download-SRA-FASTQ -c 8 -m 32 input_1/list.txt
Checking the realpath of input files.
0 input_1/list.txt
centos:centos6 ncbi/sra-tools:3.0.0
using docker
+ set -o pipefail
+ '[' input_1/list.txt '!=' '' ']'
+ cat input_1/list.txt
+ read i
+ xargs -I '{}' -P 8 bash -c '{}'
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/preprocessing~download-SRA-FASTQ/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD  -u 2007:600 -i --rm ncbi/sra-tools:3.0.0  fastq-dump --split-3 --gzip --outdir fastq ERR8701941'
+ read i
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/preprocessing~download-SRA-FASTQ/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD  -u 2007:600 -i --rm ncbi/sra-tools:3.0.0  fastq-dump --split-3 --gzip --outdir fastq ERR8701940'
+ read i
Read 138794 spots for ERR8701941
Written 138794 spots for ERR8701941
Read 190493 spots for ERR8701940
Written 190493 spots for ERR8701940
+ '[' '' '!=' '' ']'
+ post_processing
+ '[' 1 = 1 ']'
+ echo 0
+ exit
PID: 265105